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Okay, that zip file count is most likely your problem. Here's how you fix it. Sync your iPhone. Sync your desktop. Go do something else for 61 minutes. Sync your iPhone again. Sync your desktop again. Sync the iPhone one more time and have a look at the zip file count -- it should be a much smaller number!

Do you typically not having OmniFocus running on your Mac when you are using the iPhone, and vice versa? The auto-compaction code runs when it sees that all the clients have been in sync for an hour (this is protection against a client having a hard time writing out the sync data in a timely fashion, such as an iPhone in a place where reception is marginal). If you always have only one or the other active, there will be fewer occasions when that set of conditions is met, and the zip file count will continue to build up. Each one represents some sort of change to the database, and that history needs to be kept until all the clients using can agree that they are all in sync and none of it might have to be unwound.

You can find the size of your database by looking at the OmniFocus.ofocus file in your Library/Application Support/OmniFocus folder in your home directory. It might just be called OmniFocus depending on your Finder settings. For some more interesting stats, install and run Toadling's excellent Count Database Items script found here.