I'm running a newly installed and configured openVAS 5 on CentOS 6 machine.  I 
made sure I'm running nmap 5.51.

My "openvas-check-setup returns:

openvas-check-setup 2.2.0
Test completeness and readiness of OpenVAS-5

Please report us any non-detected problems and
help us to improve this check routine:
http://lists.wald.intevation.org/mailman/listinfo/openvas-discuss

Send us the log-file (/tmp/openvas-check-setup.log) to help analyze the problem.
Use the parameter --server to skip checks for client toolslike GSD and 
OpenVAS-CLI.
Step 1: Checking OpenVAS Scanner ...
OK: OpenVAS Scanner is present in version 3.3.1.
OK: OpenVAS Scanner CA Certificate is present as  
/var/lib/openvas/CA/cacert.pem.
OK: NVT collection in /var/lib/openvas/plugins contains 30428 NVTs.
  WARNING: Signature checking of NVTs is not enabled in OpenVAS Scanner.
  SUGGEST: Enable signature checking see
  http://www.openvas.org/trusted-nvts.html).

Step 2: Checking OpenVAS Manager ...
OK: OpenVAS Manager is present in version 3.0.5.
OK: OpenVAS Manager client certificate is present as 
/var/lib/openvas/CA/clientcert.pem.
OK: OpenVAS Manager database found in /var/lib/openvas/mgr/tasks.db.
OK: Access rights for the OpenVAS Manager database are correct.
OK: sqlite3 found, extended checks of the OpenVAS Manager installation enabled.
OK: OpenVAS Manager database is at revision 56.
OK: OpenVAS Manager expects database at revision 56.
OK: Database schema is up to date.
OK: OpenVAS Manager database contains information about 29686 NVTs.
OK: xsltproc found.

Step 3: Checking OpenVAS Administrator ...
OK: OpenVAS Administrator is present in version 1.2.1.
OK: At least one user exists.
OK: At least one admin user exists.

Step 4: Checking Greenbone Security Assistant (GSA) ...
OK: Greenbone Security Assistant is present in version 3.0.3.

Step 5: Checking OpenVAS CLI ...
OK: OpenVAS CLI version 1.1.5.

Step 6: Checking Greenbone Security Desktop (GSD) ...
OK: Greenbone Security Desktop is present in Version 1.2.2.

Step 7: Checking if OpenVAS services are up and running ...
OK: netstat found, extended checks of the OpenVAS services enabled.
OK: OpenVAS Scanner is running and listening on all interfaces.
OK: OpenVAS Scanner is listening on port 9391, which is the default port.
OK: OpenVAS Manager is running and listening on all interfaces.
OK: OpenVAS Manager is listening on port 9390, which is the default  port.
OK: OpenVAS Administrator is running and listening only on the local interface.
OK: OpenVAS Administrator is listening on port 9393, which is the default port.
OK: Greenbone Security Assistant is running and listening on all interfaces.
OK: Greenbone Security Assistant is listening on port 9392, which is the 
default port.

Step 8: Checking nmap installation ...
OK: nmap is present in version 5.51.

Step 9: Checking presence of optional tools ...
OK: pdflatex found.
OK: PDF generation successful. The PDF report format is likely to work.
OK: ssh-keygen found, LSC credential generation for GNU/Linux targets is likely 
to work.
OK: rpm found, LSC credential package generation for RPM based targets is 
likely to work.
WARNING: Could not find alien binary, LSC credential package generation for DEB 
based
  targets will not work.
SUGGEST: Install alien.
OK: nsis found, LSC credential package generation for Microsoft Windows targets 
is likely to work.

It seems like your OpenVAS-5 installation is OK.

If you think it is not OK, please report your observation and help us to 
improve this check routine:
  http://lists.wald.intevation.org/mailman/listinfo/openvas-discuss

Please attach the log-file (/tmp/openvas-check-setup.log) to help us analyze 
the problem.

An Nmap scan against my target (from my nmap server) reports:

[admin@openVAS1 Desktop]$ nmap -p 1-65535 -T5 x.x.x.x
Starting Nmap 5.51 ( http://nmap.org ) at 2013-04-18 12:34 PDT
Nmap scan report for test3.test3.com (x.x.x.x)
Host is up (0.024s latency).
Not shown: 65531 closed ports
PORT     STATE SERVICE
22/tcp   open  ssh
23/tcp   open  telnet
1506/tcp open  unknown
1513/tcp open  fujitsu-dtc

But an openVas scan does not report ports 1506 0r 1509 (copiec from the GSAD 
webUI):

Port summary for x.x.x.x
Service (Port)    Threat
general/icmp                     Low
general/CPE-T                   Log
general/HOST-T                Log
general/tcp                        Log
snmp (161/udp)               Log
tftp (69/udp)                     False Positive

...

general/tcp
Log (CVSS: 0.0)

NVT: Checks for open tcp ports (OID: 1.3.6.1.4.1.25623.1.0.900239)
Open TCP ports: [None found]

A scan from a collegue's openVAS machine reports those ports AND 
vulnerabilities releated to them, my machine does not.  I have compared the 
NMAP sections of the scan configs and they are the same
Any ideas why my openVAS does not report those ports??




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