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I second this behavior. I'm experiencing the exact same thing.

What I'm doing for now is a weekly maintenance routine:

1. Make sure all clients are synced and up to date
2. Archive old files that are 2 weeks old or older
3. Rename OmniFocus.ofocus to OmniFocus-old.ofocus on my webDAV
4. Run coalesce database script
5. Re-sync all clients choosing Use Server File

I'd rather an OmniFocus update fix this problem. Until then, I've taken matters into my own hands.