mail mailscanner[3204]: SpamAssassin timed out and was killed
After googling for a while, I found that this could be caused by not enough RAM on the server. I decided to increase the RAM and test again. No difference: spam still got high score and was marked as "not spam".
Blah, that's a VERY uncommon cause of the SA timeout message with mailscanner.
The usual cause is bayes expiry.. set bayes_auto_expire to 0 in your spam.assassin.prefs.conf and add a daily cron job to run sa-learn --force-expire.
I'd also suggest upping the default spamassassin timeout in MailScanner.conf. It's absurdly too short for any bayes-enabled version of SA.
