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I've had this same problem for quite a while, and it bugs the crap out of me! Let me know if you find anything out from the support ninjas--I don't have time to go that route at the moment.

The other thing I've tried in the past to fix it is to "Rebuild Database..." from the "File" menu, but I don't believe that's ever worked.

I sync from my iPhone over WebDAV, not Bonjour, so it's not a Bonjour-specific problem.