OK, this sounds strange. By your description I'm almost certain you have got a double installation of SpamAssassin running. It'd be interesting to have a look at your headers, but I wonder if you've got the mail running through BOTH because they are separate installations??? Sounds weird, but may be possible depending on how the proxy is behaving.
But I think you're playing with fire having multiple installs, and the possibility of breaking something so that all of a sudden your queue freezes b/c amavisd is not managing to get things thru the filters is a real possibility. There have been other threads discussing updating the spamassassin install within /opt/zimbra; I believe they revolved around installing the spamassassin utilities (like sa -update) into the Zimbra installation directory. Unfortunately I'm having trouble coming up with the right search terms to find the thread I know I've seen; perhaps another user will have better luck. At any rate, I can't testify to how well this works because I have not tried it. There is a
wiki article about updating ClamAV; I suspect something similar can be done with SpamAssassin as well.
The real issue, getting SpamAssassin updates more frequently than the Zimbra package updates, is partially addressed by this bug, which you should consider visiting and voting for:
Bug 15137 - Breakout RPM packages for ClamAV, SpamAssassin and Others to allow out of cycle updates
There are other threads on this forum discussing the topic as well, particularly this one:
Zimbra ClamAV Security Updates?
Bottom line, I understand why you want to do this, and so do some others. I think perhaps instead of the above thread, a bug/RFE should be filed requesting that the necessary updater tools for SA and Clam both should be integrated into the Zimbra install; feel free to file such a bug if you wish, or I'll do it on the strength of a bit more discussion/feedback.
Cheers,
Dan