KCWookie, I'm sorry for the trouble this is causing!
We're seeing reports of this problem in our applications as well as in Apple's iWork applications for the iPad. It appears that PDFs produced on the iPhone OS work there and in OS X's Preview.app.
Unfortunately, the embedded font information is not rendering properly in just about any other PDF viewer. (Anecdotally, we've heard that Helvetica Neue works better than standard Helvetica, if that helps.)
We have a bug open on this issue in our tracker, and we've communicated the problem to Apple. Unfortunately, this is very unlikely to be something we can fix in our own code; we believe it'll need to be fixed by a future Software Update for iPads.
There's some more information
here on Apple's support forums, if it helps.
As a workaround in the meantime, if you have OmniGraffle for the Mac, you can create the document on the iPad, then perform the export using your Mac instead. Again, we're really sorry for the trouble this is causing.