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I'm another person with the runaway zip file problem: 194 projects, 394 actions, 1266 zip files. Startup on the iPhone takes about 7 seconds. Sync'ing takes ... a long time.

I use OmniFocus with one Macbook Pro and one iPhone. I usually sync them twice or more times a day, and I leave OmniFocus Mac running in the background for 8+ hours most days. I sync via WebDAV (box.net).

Sync on the iPhone often fails because it goes to auto-lock while sync'ing and when I unlock it the connection has failed.

I've tried the sync-all-devices-in-consecutive-hours thing, and it did't help.

I've repeatedly tried to reset the database on the iPhone and it crashes (boots me to the home screen).

I just tried Brian's "force a compaction" strategy, and it didn't appear to do anything. I'll try it again.