[Toadling]

Have you checked what clients you have registered for syncing? Perhaps you have a stale client?

Go to OmniFocus -> Preferences -> Sync and click on the "Show Clients" button. Try to identify all the machines listed and make sure they've each been synced in the last few days. If any of them haven't, that's probably what's preventing your database from compacting.

To resolve the situation, you can either sync the stale client or just unregister it. Of course, any un-synced changes on the unregistered client will not be merged, so watch out for that.

Hope this helps.

-Dennis