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Exporting a whole document PDF with the current Mac App Store version of OmniGraffle Pro (4.5.2) the pasted vector graphics are not included into the PDF (Printing a PDF is working but there one can only have one sheet size so it didnít work for me as a workaround). I downloaded the DMG Version of the same version (4.5.2) and it worked there. Please fix the App Store version.

OS X 10.8.3