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I'm really sorry for the trouble this is causing! I'm not on the OmniGraffle team, but if you let the support ninjas know what version of the app you're using, and what version of Mac OS you have installed, they should be able to help.

In general, it sounds like something isn't happy with the transparency information in the image. If you color some text in TextEdit with similar transparency settings, what happens?

As a random shot in the dark - one thing we've seen cause this in the past is where the printer drivers work fine with carbon apps like Microsoft Office, but Cocoa ones have trouble. OmniGraffle and TextEdit are both cocoa apps, so if you see trouble there as well, going to the manufacturer's website for updated drivers *may* help.