If you create something like a pedal staff and 'mute' it, then export it to a MIDI file, you'll notice all the pedal events are gone. The best way to get around this is to check the 'muted' attribute of every note in that staff.
Good point. I'm not familiar with how pedal events work (being a singer) - I wonder if the behavior has been that way all along?
Correction:
...The best way to get around this is to check the 'muted' attribute of notes in the staff, instead of muting the staff.