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No inherent technical problem with PDFs, it's just that the file format is often used to store lots of high-rez image data that can quickly use up more memory than the iPad is willing to let OmniGraffle have access to.

Taking some PDF with a whole mess of layers and flattening it down to a PNG means that it uses a lot less memory. :-)

Creating stencils in the iPad app is something we're very interested in adding; it just didn't make it in for the initial release.

Which stencils on graffletopia are you having trouble with? We may be able to help or offer alternatives...