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I just set the canvas on a document to be 12 inches by 12 inches (864 pixels on a side), then did an export to PDF and opened the resulting file in Preview on my Snow Leopard system. Got a ruler out and measured the size of the window after selecting View->Actual Size and it turned out to be slightly undersized at 11 13/16" across. That is much larger than the window shown in OmniGraffle, and I suspect that might be the source of the confusion. Bring up the ruler in OmniGraffle and get out a ruler of your own for comparison. On my machine (27" iMac) 12" on the OG ruler only takes up 7 7/8" on my ruler, which is what one might expect on a display that is about 109 ppi instead of the nominal 72.