Sure it's ethical to bump. Sorry I didn't notice this one sooner since spam is one of my hot buttons. . .
I'm guessing here, but where do you have your settings tweaked? If in /opt/zimbra/conf/spamassassin/local.cf (or other .cf files--which ones?), are there any odd permission issues on those files? The tag/kill percentages--have you set them in the admin gui, at the command line, or by editing files?
Except for that change in the gui, I have made all my changes in local.cf (and I keep a backup of it since it gets overwritten with every upgrade) and it has straight-across read permissions only. I don't touch any of the other cf files except to read them and learn syntax of things that I then override with settings in local.cf. That process has worked reliably for me.
Since you are network edition you have the right to get tech support right from the horse's mouth too, remember.
Cheers,
Dan