It sounds like a config issue. It would pay to do a "spamassassin -D --lint". This will produce a lot of output, but it is worth reading and understanding all of the information, to be able to parse it for errors.
Actually just 'spamassassin --lint' might be a good thing to do, being sure to run under the corredct usercode. This should have no output if things are right.
Loren
