I have MainStage hooked up to a MOTU 828mkII and an Oxygen61 keyboard. When I play software instruments it works fine. When I create a channel strip with external instruments it freaks out whenever I use pitch bend. Example: I have a Yamaha Motif XS rack plugged into the MIDI out on the MOTU. When I define this instrument in the channel strip and play I hear all the notes just fine. I apply pitch bend and can hear no difference in sound until I get to the top of the PB range then the sound suddenly jumps an octave. Releasing PB brings the sound down but not to the original note. It's off by a second and I have to cycle the power on the synth to get it back to normal pitch. I've tried this with different MIDI interfaces, synths, and controllers and still the same effect. This appears to be a pretty serious bug and I haven't found any way around it.
Sorry can't help, All I can say is I have had the same problem. with pitchbend on external instruments. Infact if I use it It can shut down the whole program.
I believe this problem as been reported as a bug. I experienced the same problem with trying to control an external VL70m synth with my EWI.
What I did to solve the problem was set up midi pipe and connect to the synth directly outside of MS2 which lets me control it properly. I use my EWI to send program changes to MS2 so I also filtered out program changes in midi pipe so the VL70m only received its program changes from MS2.