I am having some issues with getting bayes to work using spamc/spamd.
I'll admit I don't know the answer to your question, but you left out some important details:
1) what version of SA do you have?
2) have you upgraded between versions? if so, what did you have before?
However, it is strange that spamassassin works with it, but spamd doesn't... I'd check for duplicate copies of spamassassin, one in /usr/bin and one in /usr/local/bin.. if you've got that, make sure you're always using the same version or blow the errant one away..
note that on many linux distros by default normal users will get the /usr/local/bin copy, and root will not, so if you have this problem, when root launches spamd the path will be different than when an unprivileged user runs plain spamassassin.
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