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We fixed the issue where quitting frequently would cause sync problems. So don't worry about that. But it still sounds like something's going wrong here.

1) What server are you syncing to? MobileMe? Another public WebDAV service? WebDAV set up on one of your own machines?
2) Are the Mac Mini and the Powerbook connecting to the internet the same way from the same place? Or is one at home and the other at work?
3) Are there any OmniFocus error messages in the Console?