Thanks for all the Help,
I managed to disable the rootcheck manually.
It appeared that I had a problem with publishing the document and the 
permissions of the file.

On Thursday, April 14, 2016 at 1:54:29 PM UTC+3, eyal gershon wrote:
>
> Hey,
>
> I tried to disabled the rootcheck on one of the servers.
> I have added the following line to the agent.conf file - 
>
> <rootcheck>
>     <disabled>yes</disabled>
> </rootcheck>
>
> and after I am restarting the service I get the following output - 
> Starting ossec-hids: 2016/04/14 06:16:27 ossec-rootcheck: Rootcheck 
> disabled. Exiting.
> ossec-syscheckd: WARN: Rootcheck module disabled.
>
> and a few min later I see in the logs that the rootcheck is running again.
> any one have an idea why did I miss?
>

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