This has been an ongoing problem for a number of years on windows computers.
I think I have found one of the culprits, and can replicate the problem easily.
If I open an Invoice from a supplier who uses MYOB accounting to produce the pdf document, the next time I launch FileMaker the fonts will have been corrupted. I can only assume MYOB are using an old version of the .pdf engine to create the invoices.
Not much we can do about that, but it might give FileMaker somewhere to talk to help eliminated it.