This has happened at least 4 times where a CS6 document is opened the fonts are auto loaded from the Document Fonts folder which appear to load correctly. Visually on the screen No missing font messages and the internal preflight reports No Errors. When you Export to PDF, No Font errors or missing fonts messages appear on the screen and when you open the PDF you created all the fonts are missing and have been replaced with your default font. Try exporting it again same results No Errors, Still a Bad PDF, reboot the Mac and then load and export the same file and the PDF is perfect. It has happened on 2 different Mac work stations running on a Prinergy server. Anyone have an idea why this happening? But more importantly why are the safeguards built into Indesign not catching this like it normally would do?
What Mac O/S are you running? What fonts are you using? How are you viewing the PDF?
One possible reason is corrupt font cache. When the Mac is rebooted, the font cache is deleted and rebuilt as necessary.