You should probably check that none of your ham (i.e. non-spam) messages contains SPAM_99 or SPAM_999. It can happen when spammers poison your bayes database, and increased score in that case might lead to legitimate mail being misclassified as a spam.That's a great call, thanks. I grepped my mail files and didn't find any SPAM_99 headers in any of them.
You should be looking for BAYES_99 and BAYES_999 in your corpus. Best, Dave