Okay, I answered my own question. I read that Microsoft sent out corrupt versions of Arial and Times with OS X and Apple has not corrected it. There was an updated link from Microsoft, but it's now no longer being offered. SOOO... rather than jumping through hoops, I just placed all instances of Times Phonetic Alternate in it's own folder in the fonts folders so the system can't activate it and it magically displays the type in regular Times.
Tada!