Hi all, here's my problem, AGAIN !
First, run spamassassin --lint
If there are any complaints about your configuration files, fix them. Minor typos can cause bad side effects.
If that doesn't help.. try running a message through SA with the debug output turned on. The first 10 or so lines of debug should tell you what directories SA is using for config files. It may also give you more general information about what it's doing as it parses them.
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