If you're running SA 3.2.3 or higher, there were some new exit codes added that the Domino Spamassassin code doesn't know about. To fix it on my server, I opened my mail template (mail85.ntf) in the Domino designer, opened the SpamAssassin script library and edited the "mlngRunSpamAssassin" function.
Scroll all the way down to the bottom and find this section:
Loop Until blnRanSpamAssassin<br/>
mlngRunSpamAssassin = lngExitCode <br/>
Exit Function<br/>
Add this line right under the Loop - "If lngExitCode > 1 Then lngExitCode=1"
The modified section of the function should look like this:
Loop Until blnRanSpamAssassin<br/>
If lngExitCode > 1 Then lngExitCode=1<br/>
mlngRunSpamAssassin = lngExitCode <br/>
Exit Function<br/>
That should fix it for you.
-=Phil