Try saving your files without generating external binary morph targets (turn it off in General Preferences) and see it fixes the problem. Do load the PP2012 service pack update, it may correct some of your issues. PMD's are known to become corrupted and, IIRC, those issues were addressed and corrected in PP2014. I, personally, do not use PMD generated files when saving characters back to the Library. However, if you plan to distribute character sets, it is a good idea to incorporate PMDs for final file size and speed.