Mainstage doesn't care how you connect the the FS-6 because it doesn't "know" how you do it. Mainstage cares just for MIDI data sent by the MOXF6; and obviously this data differs depending on the way the pedal is connected. But that's not a Mainstage problem; that's a keyboard problem.
A good first step would be to monitor which data is being sent in both the TR and TRS scenarios.
It's also not completely clear to me how (or whre) you connect it in the TRS scenario.