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I'm not on the OmniGraffle team, but I remember overhearing discussion of this last week. My memory is that the app's asking for access to the "Me" contact card for the logged in account. It does so in order to set the "Creator" metadata in the XML of the documents you create.

If you save a Graffle doc as a flat file, then drag it to TextWrangler, BBEdit, or a similar app, you can search for "<key>Creator</key>" to locate the info in question. Hope that helps!