Maybe you could try this:
- Unplug the pedals.
- Delete the Controls profile for the pedals.
- Reboot your computer
- Plug the pedals back in and wait for the notification as described above.
- Add a new profile for the pedals. Make sure the axes bindings are exactly as you had them.
I have CH Pro pedals, too, and they are working quite well after SU12. Do your pedals work for non-PMDG planes? If so, is there a separate PMDG control setting? Is there a PMDG forum where you can ask the same question?