When I do a: "sa-learn --mbox --spam kill" I get:
Learned from 0 message(s) (127 message(s) examined).
First, I'd check for file permission issues.. make sure you've got the ability to create files in ~/.spamassassin. It's really easy to do something like "chmod 600 .*" in your home directory and whack the x bit on your .spamassassin directory.
Usually that resorts in a "cannot create temp lockfile" error message, but it's worth a check.
After that, you might try looking at sa-learn's debug output.
sa-learn -D --mbox --spam kill
This should tell you why the messages aren't being learned. i.e.:
debug: [EMAIL PROTECTED]: already learnt correctly, not learning twice
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