A couple of fixes:
1) http://www.macupdate.com/info.php/id/14470/font-finagler
Validate your fonts. Load Font Book (Applications > Font Book) and select all your fonts (Command-A), and then choose File > Validate Fonts. Remove any fonts that are tagged with errors or warnings.
Clear your font cache. Download and install FontNuke and follow the instructions.
2) If your pdf files have missing or garbled text, open terminal and kill the ATSSERVER process with the following command line (substitute in your user name):
killall -u YourUserName ATSServer
After running this command, ATSServer will relaunch right away. If you close the afflicted pdf file and reopen it all the fonts will display properly.