I'd urge you to contact the support ninjas for help with this using Help → Send Feedback in the desktop app. They won't be able to respond until Monday morning in Seattle.
Alternatively, you could try this:
- Turn off syncing on the desktop app.
- Choose File → Backup Database to make sure you have a fresh backup.
- Log on to me.com using your web browser.
- Click the iDisk icon in MobileMe
- Navigate to Document → OmniFocus.ofocus
- With OmniFocus.ofocus selected, click the gear icon (top center) and choose Rename
- Give a new name to your OmniFocus data, say "OldOmniFocus.ofocus". Now neither the Mac nor your phone will touch that data. It's still available if you need it to recover.
- In OmniFocus on your iPhone, turn on syncing to MobileMe. You'll probably have to enter your MobileMe user name and password. (If MobileMe syncing is already on for the phone, you can skip this step.)
- Tap the sync icon in OF for iPhone. You should get a warning about there being no data on the server. Choose to upload the phone database to the server.
- Once the phone has successfully synced, you're ready to move the data from MobileMe to your Mac.
- In OF on your Mac, turn on syncing with MobileMe.
- Start a sync from your Mac. You should be prompted that the database are incompatible. Choose to replace your Mac data with the data from MobileMe. This should be the same data that was on the iPhone. Once this sync completes the iPhone data should be everywhere.