On rare occaisons, an upgrade to FileMaker or your OS will bring to light a problem with your file that did not cause issues with the older version.
Run a recover on the file and see if the recovered copy works.
There also have been a few reports of issues with save as PDF and FileMaker 12 and I am monitoring a thread to see if FileMaker confirms that report or not.
I am starting to have this issue now as well. Has there be a fix/work around for this found?