PDF Font Issues

I recently added some new fonts to my directory.  Since then, I have had font issues with my pdf's and previews where the characters are illegible.  I have tried using disabling fonts on Font Book for pdfs, and tried using Font Finagler and FontNuke to clear all font caches.  The problem only seems to effect pdf's.  I am operating on OSX 10.6.7.  Does anyone have any suggestions that might fix this problem. 

I was getting a "Missing Font" message and the explanation on the forum is that a bug in 10.6.7 caused the OS to UNEMBED fonts in PDF files!
Don't know who said that, but it's incorrect.
I built a simple text document with three lines of text. Opened three fonts not on the system, applied one each to a line of text and saved a PDF using Apple's built in PDF generator.
I then disabled the fonts and deleted them. With no fonts to find and the comment being true that fonts are not embedded, the PDF should display incorrectly. It didn't. I looked exactly as it should, meaning the fonts had to be embedded in the file.

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