Jesse, 
Are you running the scan from a command prompt using a .nessusrc policy
file that was created in the Nessus GUI client and exported?  If you
did, chances are that the SCANNER_SET section within the .nessusrc file
is not being written during the export process.  This happened to me in
version 3.0.6 and was supposed to be fixed in the current version of
Nessus.  I resolved the issue by manually going into the .nessusrc
policy file and adding this section:

begin(SCANNER_SET)
10180 = no
10277 = no
10278 = no
10331 = no
10335 = yes
10841 = no
10336 = no
end(SCANNER_SET)  

Hope this helps.

Richard

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Subject: Nessus Digest, Vol 56, Issue 18

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Today's Topics:

   1. WARNING : no port scanner was enabled during the scan. This
      may lead  to incomplete results. (Jesse Mauntel)


----------------------------------------------------------------------

Message: 1
Date: Fri, 20 Jun 2008 13:57:39 -0700
From: "Jesse Mauntel" <[EMAIL PROTECTED]>
Subject: WARNING : no port scanner was enabled during the scan. This
        may lead        to incomplete results.
To: <[email protected]>
Message-ID:
        
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="us-ascii"

We just rebuilt our Nessus server as a RHEL 5 system and upgraded Nessus
from 3.0.6 to 3.2.1.  Now when we initiate a scan from our other system
(client) we get the following message in our results:

        WARNING : no port scanner was enabled during the scan. This may
lead to incomplete results.

What causes this?  Is there any way to correct it without upgrading the
Nessus client?
 
Thanks,
 
- Jesse
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