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:<
Apple knows about the problem and isn't planning to fix it (I had a faculty member spend a lot of time testing and submit a bug to Apple). Their claim is that PDFTeX is embedding the fonts incorrectly, and they have fixed the Apple PDF library to be more strict about what it will and won't accept, which means that you will continue to see problems with PDF documents created with PDFTeX in Preview, TeXShop, or other tools that display PDF using Apple's PDF engine. Unfortunately, they weren't at all clear about exactly what it is that PDFTeX is doing wrong, which makes fixing it or even reporting the bug to the PDFTeX developers problematic. Note that Adobe's Acrobat or Reader applications can often display these documents without any problems; presumably Adobe's error-checking is more liberal than Apple's.
You can actually recover from this problem without rebooting, although you may see it recur with the same document in the same session. You need to run
atsutil server -shutdown
which will kill the Apple Type Services server daemon (ATSServer) and spawn a new instance, coincidentally rebuilding its cache files.