Can you describe the setup? I'm assuming that you have some Avid or M-Audio interface that is sync'ing MIDI back and forth to the Yamaha... If the Yamaha is transmitting MTC and ProTools is reading MTC (at the same frame rate), then it should sync up.
To be fair, I run Native and not SE, so it's possible that SE doesn't support MIDI sync. Anyone out there on SE know if it will read MTC?