What version of FileMaker Pro are you using? If you used FileMaker Pro 15 version 2 , that version had problems with fonts that where old style. You need to update to version 3
FileMaker Pro Advanced 14.0.1. None of the 15th versions work properly for me, so I downgraded to 14.
By the way, fonts are not older, they are new.
Try making a brand new layout (do not duplicate an existing layout) and put some text objects on the layout with different fonts. Print to PDF and see what happens.
If it works it could be a corrupted layout.
Edit: Try it with a newly created file too.
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Thanks for suggestion.
Meanwhile, I was able to find the solution myself, and I am going to share it:
As fonts that failed to work were Open Type Fonts (.otf) instead of True Type Fonts (.ttf)
1) Convert .otf font to .ttf using: Convert otf to ttf | Everything Fonts
2) Re-open Filemaker and it works like a charm!
Open type fonts have not been supported by FileMaker for several versions.