[whpalmer4]

Patrick, if Dennis' suggestion doesn't yield some improvement, I'd suggest emailing or calling the support ninjas. I've seen some behavior relating to syncing perspectives in Snow Leopard that seems to only happen on my Snow Leopard machine, and depending on the order that various machines are synced, may prevent database compaction from taking place. It's impossible to say conclusively whether that is your issue from the data provided, but if it is, perhaps the additional data points could help find the cause of the problem. I think my case is probably fairly rare, or they would have had more reports of it, so I'm going to speculate that when you upgraded one or more of your machines, something happened to fool OmniFocus into creating a new client in the sync database instead of using the old one, and it is the presence of the old one that is keeping the database from compacting, as Dennis suggested. Fortunately, if it does turn out to be a stale client, the fix is very easy!

Which version(s) of OmniFocus are you using?