Thanks for posting!
I'm having some trouble replicating this behavior. I created a new database in FileMaker Pro 11v3 on OS X 10.6 with a text box and a field, both using the Verdana font. I then saved a PDF to confirm that everything showed up as expected, closed FileMaker Pro and moved the FileMaker Pro 11v3 folder from the Applications folder to a subfolder within Applications named •. After saving a new PDF, I did not observe any change in result.
Is there something else I should be doing in addition to the above? Can you reproduce this in a new database? What about on a different machine entirely?