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I had some difficulty at first getting my database to sync to my new iPhone 3GS via MobileMe. It turned out that OmniFocus on my iPhone was stalling because it apparently failed to authenticate with my MobileMe account and didn't prompt me for a password.

I worked around it by switching OmniFocus for iPhone to using Bonjour, then switched back to MobileMe and manually configured it from the iPhone. I then got the MobileMe password prompt in OmniFocus and proceeded successfully.

I'm not sure if I could reproduce the issue again; I wasn't paying very close attention along the way, so I might even be missing a step. But I thought I'd post my experience here anyway. Maybe it'll help someone else.