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How does it fail? I don't see how you could fail with the built-in stencil search gadget just tap the Stencil menu icon at the upper right, type in your search term(s), choose a stencil and tap the Download button.

Or are you going to the Graffletopia website from Safari? Find a stencil, tap the Download button, tap the Open in OmniGraffle button. I don't have an iPad 3, but I didn't see anything on either path that looked like it would fail with a different screen resolution...