I am running into an issue where the windows agent is installing and the 
service starts, and after the initial syscheck scan the service receives a 
shutdown command and has to be manually restarted.

Here is the *agent.conf:*


<agent_config>
  <!-- Rootcheck - Policy monitor config -->
  <rootcheck>
    <windows_audit>./shared/win_audit_rcl.txt</windows_audit>
    <windows_apps>./shared/win_applications_rcl.txt</windows_apps>
    <windows_malware>./shared/win_malware_rcl.txt</windows_malware>
  </rootcheck>  


   <!-- Syscheck - Integrity Checking config. -->
  <syscheck>
  
    <!-- Default frequency, every 20 hours. It doesn't need to be higher
      -  on most systems and one a day should be enough.
      -->
    <frequency>72000</frequency>

    <!-- By default it is disabled. In the Install you must choose
      -  to enable it.
      -->
    <disabled>no</disabled>  


    <!-- Default files to be monitored - system32 only. -->
    <directories check_all="yes">%WINDIR%/win.ini</directories>
    <directories check_all="yes">%WINDIR%/system.ini</directories>
    <directories check_all="yes">C:\autoexec.bat</directories>
    <directories check_all="yes">C:\config.sys</directories>
    <directories check_all="yes">C:\boot.ini</directories>
    <directories check_all="yes">%WINDIR%/System32/CONFIG.NT</directories>
    <directories check_all="yes">%WINDIR%/System32/AUTOEXEC.NT</directories>
    <directories check_all="yes">%WINDIR%/System32/at.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/attrib.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/cacls.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/debug.exe</directories>
    <directories 
check_all="yes">%WINDIR%/System32/drwatson.exe</directories>
    <directories 
check_all="yes">%WINDIR%/System32/drwtsn32.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/edlin.exe</directories>
    <directories 
check_all="yes">%WINDIR%/System32/eventcreate.exe</directories>
    <directories 
check_all="yes">%WINDIR%/System32/eventtriggers.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/ftp.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/net.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/net1.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/netsh.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/rcp.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/reg.exe</directories>
    <directories check_all="yes">%WINDIR%/regedit.exe</directories>
    <directories 
check_all="yes">%WINDIR%/System32/regedt32.exe</directories>
    <directories 
check_all="yes">%WINDIR%/System32/regsvr32.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/rexec.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/rsh.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/runas.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/sc.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/subst.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/telnet.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/tftp.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/tlntsvr.exe</directories>
    <directories check_all="yes">%WINDIR%/System32/drivers/etc</directories>
    <directories check_all="yes">C:\Documents and Settings/All Users/Start 
Menu/Programs/Startup</directories>
    <ignore 
type="sregex">.log$|.htm$|.jpg$|.png$|.chm$|.pnf$|.evtx$</ignore>


    <!-- Windows registry entries to monitor. -->
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Classes\batfile</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Classes\cmdfile</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Classes\comfile</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Classes\exefile</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Classes\piffile</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Classes\AllFilesystemObjects</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Classes\Directory</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Classes\Folder</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Classes\Protocols</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Policies</windows_registry>
    <windows_registry>HKEY_LOCAL_MACHINE\Security</windows_registry>
    <windows_registry>HKEY_LOCAL_MACHINE\Software\Microsoft\Internet 
Explorer</windows_registry>


    
<windows_registry>HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session 
Manager\KnownDLLs</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\SecurePipeServers\winreg</windows_registry>

    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunOnce</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunOnceEx</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\URL</windows_registry>
    
<windows_registry>HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Policies</windows_registry>
    <windows_registry>HKEY_LOCAL_MACHINE\Software\Microsoft\Windows 
NT\CurrentVersion\Windows</windows_registry>
    <windows_registry>HKEY_LOCAL_MACHINE\Software\Microsoft\Windows 
NT\CurrentVersion\Winlogon</windows_registry>

    <windows_registry>HKEY_LOCAL_MACHINE\Software\Microsoft\Active 
Setup\Installed Components</windows_registry>



    <!-- Windows registry entries to ignore. -->
    
<registry_ignore>HKEY_LOCAL_MACHINE\Security\Policy\Secrets</registry_ignore>
    
<registry_ignore>HKEY_LOCAL_MACHINE\Security\SAM\Domains\Account\Users</registry_ignore>
    <registry_ignore type="sregex">\Enum$</registry_ignore>
  </syscheck>    

  <active-response>
    <disabled>yes</disabled>
  </active-response>

</agent_config>

*ossec.conf:*

<!-- OSSEC Win32 Agent Configuration.
  -  This file is compost of 3 main sections:
  -    - Client config - Settings to connect to the OSSEC server. 
  -    - Localfile     - Files/Event logs to monitor.
  -    - syscheck      - System file/Registry entries to monitor.
  -    - Oct 10, 2012 - Removed all default settings in this file, all 
settings are push via agent.conf JMoles
  -->

<!-- READ ME FIRST. If you are configuring OSSEC for the first time, 
  -  try to use the "Manage_Agent" tool. Go to control panel->OSSEC Agent
  -  to execute it.
  -
  -  First, add a server-ip entry with the real IP of your server.
  -  Second, and optionally, change the settings of the files you want 
  -          to monitor. Look at our Manual and FAQ for more information.
  -  Third, start the Agent and enjoy.
  -
  -  Example of server-ip: 
  -  <client> <server-ip>1.2.3.4</server-ip> </client>
  -->


<ossec_config>


</ossec_config>


<!-- END of Default Configuration. -->


 <ossec_config>
   <client>
      <server-hostname>xxx.xxx.com</server-hostname>
   </client>
 </ossec_config>

and the* ossec log on the agent:*

2012/10/23 20:00:04 (null): INFO: System is Vista or Windows Server 2008.

2012/10/23 20:00:07 ossec-agent(1905): INFO: No file configured to monitor.

2012/10/23 20:00:07 ossec-execd(1350): INFO: Active response disabled. 
Exiting.

2012/10/23 20:00:07 ossec-agent(1410): INFO: Reading authentication keys 
file.

2012/10/23 20:00:07 ossec-agent: INFO: Trying to connect to server (*
redacted.hostname.com*/xx.xx.xx.xx:1514).

2012/10/23 20:00:07 ossec-agent: INFO: Using IPv4 for: xx.xx.xx.xx .

2012/10/23 20:00:07 ossec-agent: Starting syscheckd thread.

2012/10/23 20:00:07 ossec-agent(1702): INFO: No directory provided for 
syscheck to monitor.

2012/10/23 20:00:07 ossec-agent: WARN: Syscheck disabled.

2012/10/23 20:00:07 ossec-rootcheck: INFO: Started (pid: 2556).

2012/10/23 20:00:07 ossec-agent: INFO: Started (pid: 2556).

2012/10/23 20:00:10 ossec-agent(4102): INFO: Connected to the server (*
redacted.hostname.com*/xx.xx.xx.xx:1514).

2012/10/23 20:00:10 ossec-agent: INFO: System is Vista or Windows Server 
2008.

2012/10/23 20:00:10 ossec-agent: INFO: Started (pid: 2556).

2012/10/23 20:01:37 ossec-agent: INFO: Starting rootcheck scan.

2012/10/23 20:01:37 ossec-agent: No winaudit file configured.

2012/10/23 20:01:37 ossec-agent: No winmalware file configured.

2012/10/23 20:01:37 ossec-agent: No winapps file configured.

2012/10/23 20:01:42 ossec-agent: INFO: Ending rootcheck scan.

2012/10/24 10:34:05 ossec-agent: Received exit signal.

2012/10/24 10:34:05 ossec-agent: Exiting...

2012/10/24 10:34:06 

2012/10/24 10:34:06 (null): INFO: System is Vista or Windows Server 2008.

2012/10/25 20:19:17 

2012/10/25 20:19:17 (null): INFO: System is Vista or Windows Server 2008.

2012/10/26 11:26:52 ossec-agent(1905): INFO: No file configured to monitor.

2012/10/26 11:26:53 ossec-execd(1350): INFO: Active response disabled. 
Exiting.

2012/10/26 11:26:53 ossec-agent(1410): INFO: Reading authentication keys 
file.

2012/10/26 11:26:53 ossec-agent: INFO: Assigning counter for agent *
redacted_agentname*: '4:4735'.

2012/10/26 11:26:53 ossec-agent: INFO: Assigning sender counter: 0:518

2012/10/26 11:26:53 ossec-agent: INFO: Trying to connect to server (*
redacted.hostname.com*/xx.xx.xx.xx:1514).

2012/10/26 11:26:53 ossec-agent: INFO: Using IPv4 for: xx.xx.xx.xx .

2012/10/26 11:26:53 ossec-agent: Starting syscheckd thread.

2012/10/26 11:26:53 ossec-rootcheck: INFO: Started (pid: 2084).

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Classes\batfile'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Classes\cmdfile'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Classes\comfile'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Classes\exefile'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Classes\piffile'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Classes\AllFilesystemObjects'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Classes\Directory'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Classes\Folder'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Classes\Protocols'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Policies'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Security'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Microsoft\Internet Explorer'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session 
Manager\KnownDLLs'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\SecurePipeServers\winreg'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunOnce'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunOnceEx'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\URL'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Policies'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Microsoft\Windows NT\CurrentVersion\Windows'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Microsoft\Windows NT\CurrentVersion\Winlogon'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring registry entry: 
'HKEY_LOCAL_MACHINE\Software\Microsoft\Active Setup\Installed Components'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/win.ini'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/system.ini'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\autoexec.bat'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\config.sys'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 'C:\boot.ini'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/CONFIG.NT'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/AUTOEXEC.NT'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/at.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/attrib.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/cacls.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/debug.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/drwatson.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/drwtsn32.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/edlin.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/eventcreate.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/eventtriggers.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/ftp.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/net.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/net1.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/netsh.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/rcp.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/reg.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/regedit.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/regedt32.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/regsvr32.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/rexec.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/rsh.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/runas.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/sc.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/subst.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/telnet.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/tftp.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/tlntsvr.exe'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 
'C:\Windows/System32/drivers/etc'.

2012/10/26 11:26:53 ossec-agent: INFO: Monitoring directory: 'C:\Documents 
and Settings/All Users/Start Menu/Programs/Startup'.

2012/10/26 11:26:53 ossec-agent: INFO: Started (pid: 2084).

2012/10/26 11:26:54 ossec-agent(4102): INFO: Connected to the server (*
redacted.hostname.com*/xx.xx.xx.xx:1514).

2012/10/26 11:26:54 ossec-agent: INFO: System is Vista or Windows Server 
2008.

2012/10/26 11:26:54 ossec-agent: INFO: Started (pid: 2084).

2012/10/26 11:27:53 ossec-agent: INFO: Starting syscheck scan (forwarding 
database).

2012/10/26 11:27:53 ossec-agent: INFO: Starting syscheck database 
(pre-scan).

2012/10/26 11:27:53 ossec-agent: WARN: Error opening directory: 
'C:\boot.ini': No such file or directory 

2012/10/26 11:27:53 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/CONFIG.NT': No such file or directory 

2012/10/26 11:27:53 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/AUTOEXEC.NT': No such file or directory 

2012/10/26 11:27:53 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/debug.exe': No such file or directory 

2012/10/26 11:27:53 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/drwatson.exe': No such file or directory 

2012/10/26 11:27:53 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/drwtsn32.exe': No such file or directory 

2012/10/26 11:27:53 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/edlin.exe': No such file or directory 

2012/10/26 11:27:53 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/eventtriggers.exe': No such file or directory 

2012/10/26 11:27:53 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/rcp.exe': No such file or directory 

2012/10/26 11:27:53 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/rexec.exe': No such file or directory 

2012/10/26 11:27:53 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/rsh.exe': No such file or directory 

2012/10/26 11:27:55 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/telnet.exe': No such file or directory 

2012/10/26 11:27:55 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/tftp.exe': No such file or directory 

2012/10/26 11:27:55 ossec-agent: WARN: Error opening directory: 
'C:\Windows/System32/tlntsvr.exe': No such file or directory 

2012/10/26 11:27:55 ossec-agent: INFO: Finished creating syscheck database 
(pre-scan completed).

2012/10/26 11:28:05 ossec-agent: INFO: Ending syscheck scan (forwarding 
database).

2012/10/26 11:28:25 ossec-agent: INFO: Starting rootcheck scan.

2012/10/26 11:28:30 ossec-agent: INFO: Ending rootcheck scan*.*


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