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You did verify that other applications can successfully save when OmniGraffle cannot, right? How about OmniOutliner, which also saves packages in at least some cases? (You can download a trial copy for free if the school doesn't have a license) Obviously, testing a non-Omni, non-package-writing application (TextEdit seems like a fine choice) to make sure that the problem isn't seen there would help to show that the problem is one that Joel should be chasing. I apologize if you've already done the obvious and assumed we would know you did so before asking...