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Hmm, I am unable to reproduce this problem. Following your steps exactly, when I click the "Show in Mailbox" link in Apple Mail it seems to work fine.

Perhaps there is some kind of corruption in Mail's database? I don't know if this will help, but have you tried the Mailbox -> Rebuild command in Mail?

My gut tells me that this has nothing to do specifically with OmniFocus, but I don't really know.

-Dennis