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This is happening to me also. For the sake of helping the Omni guys out, here's how it went down for me:

I smooshed my database on Friday (using Lizard's script), and over the weekend, had no problems. Sync worked fine, and there were never more than 2 .zip files in my database.

Then last night, I did my weekly review, which meant lots of changes to projects and actions, including marking my projects as reviewed, etc. OF for the Mac was syncing all along the way. Then I synced my iPhone and all of the changes synced across just fine.

But, I was a little curious, and checked my database file on my webDAV server, and sure enough, there were over 20 .zip files!

So, I deleted the file from my webDAV, re-smooshed my local database, synced to webDAV, then synced my iPhone and chose "Use Server" when prompted. I'm now back down to 1 .zip file.