Hmmm, need to check on my own server later today, but I have this feeling that the SA database never gets any tokens expired from it. The journal is being sync'd so that is all cool. Now you have the SA binaries what you could do is take one of your emails from /opt/zimbra/store and run it through SA to see where it slows down
Code:
su - zimbra
time spamassassin -D < <path to message file>