I recorded some notes and program changes from the keyboard controller. When I look at the MIDI track in an editor, the program changes are there, yet when I play it, Pianoteq plays the notes but doesn't see or do the Prg changes.

I can't find a setting for filtering out incoming Prg Changes. Is there one? Where?

This is most probably not a problem with the MIDI mapping. The MIDI monitor window shows that Pianoteq doesn't see the Prg Changes at all. The problem is there, whatever the MIDI mapping.

As standalone, Pianoteq does respond to Prg Changes form the same keyboard controller.