My colleague suggests that texniscope is somehow to blame and that I should try purging it from my system. I really hope not to have to resort to that!
Possible clues:<
Look at the pdf in Adobe Reader under the document properties. If you have Type 3 (?) bitmap fonts for the math, you need to tell the driver to embed the proper Type 1 vector fonts into the resulting document.
I use latex with dvips then pdf on linux. It used to be I had to tell it to do this, but now it seems at least the package on ubuntu has the proper font setting.
Look on the web to tell you how to embed the proper fonts into the document.
On second thought, maybe you don't have any of the fonts installed on your system or none of your fonts are being embedded into the document.