The problem, as far as I can tell, is that as of OS v1.15 (August 2014) the Pulse 2 only changes bank via Bank LSB (CC #32). The OT ensures that, when Bank Select and Program Change parameters are set in MIDI Note Setup (function+playback), Bank Select is sent before Program Change. But MIDI Note Setup strictly adjusts Bank MSB (CC #00), so it will have no effect on the Pulse 2’s bank setting.
If you map a data entry knob to CC #32, select your bank via that knob (e.g., bank 3), start playback, and then change the program in MIDI Note Setup (e.g., program 77), the Pulse 2 will correctly change to program 377. But this will only work if you do those steps in that order manually, as it will by default send Program Change before any of the other CC messages.
Users of other external gear are struggling with this as well: Midi bank change
Very frustrating as it’s a pretty serious impediment to sequencing my Pulse 2 with the Octatrack.