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I'm having the same issue as well. I didn't realize what the possible issue is, but just as bashiri I also upgraded to Lion recently.

The exact error message I get when saving is:

The document “Untitled” could not be saved as “Untitled.graffle”. +[PDFPage pageNumber:fromPagesDictionary:pdfStorage:]: unrecognized selector sent to class 0xacb09a5c

Is there a temporary fix for this? I have no way of saving my OmniGraffle documents now :(