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I'm seeing this as well.

I think it may be "normal" for the new Omnifocus file format. Specifically, it looks like, to make synching much easier, that each task in OF is now represented as a file in the OF "file." Each of them is zipped. Thing is, the minimum file size with HFS+ looks to be around 4 KB, so each item takes 4 KB (minimum) of space. I have 560 .zip files in my .ofocus package file, and simple math gives about 2.2 MB for that. That's about what I have.

What I don't know is if OmniFocus will always leave the tasks this way, or if cleanup will address it at some point.

I can see that my Omnifocus file went from 132 KB on July 8th, 2008 and is now 2.4 MB in size. So the explosion of these same files is definitely responsible for it, but I don't know if it's by design or because cleanup of the sync items isn't happening along the way.