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When you say all are synced regularly... does that mean you are syncing and then shutting one down?

Example, syncing your home computer then shutting the home computer down when you go to work?

I found I need to leave all three OF applications up and running.
As long al all your clients have synced within an hour of each other, the compaction should happen.

You can check this by viewing the clients from the sync OF preference.

On a side note... it sounds like data compaction may be happening all the time in the beta version of OF and the new iPhone version.

If you haven't done so yet, I would send in a support request by selecting:
help -> send feedback from the OmniFocus desktop menu.