I have the same problem - I can run spamassassin from the command line OK (Windows Server 2003) so the PATH statement is correct, but when it tries to run from the agent, I get these errors:
java.io.IOException: CreateProcess: spamassassin.exe -e error=2 (318)
at SPAMASSASSIN:MLNGEXECJAVAPROCESS:24<br/>
at SPAMASSASSIN:MLNGRUNSPAMASSASSIN:100 (A process could not be created for command "spamassassin.exe -e"; make sure the command is listed in your PATH environment variable or change your SpamAssassin options (may need a file extension such as .bat or .exe))<br/>
at SPAMASSASSIN:GCHECKDOCUMENT:70<br/>
at 41E9A54:INITIALIZE:17<br/>
Could it be the java version or something like that?