When I run spamassassin --lint, I get the following error:
# spamassassin --lint config: SpamAssassin failed to parse line, skipping: smtp inet - y - - smtpd
That looks like your spamassassin site-rules directory contains other config files that do not contain SA rules.
The above looks like an inetd config file.
Run spamassassin --lint -D and see what directory SA is using as it's "site rules dir". Make sure that the only .cf files there are the ones for SA, not inetd.
If SA is using some bogus directory like /etc, try creating /etc/mail/spamassassin/ and it should shift to using that instead.
