I have found that any account on the server that has enabled spam assassin, is not receiving any mail. Any account without spam assassin enabled receives mail just fine, and when you disable spam assassin the missed mail will trickle back into the email box.

The temporary solution naturally is to not use spam assassin, but I have clients that really want to have it filter their mail.

I have upgraded my perl to 5.8.8 as per some of the other tips I was reading about spam assassin, but that did not fix my problem with it.