Things to try:
With the I-Pac unplugged and a regular keyboard connected, does pressing 1 and then 2 cause MAME to exit? If so, look at your MAME or Arcade OS settings.
If not, set some other shift functions on the I-PAC and see if these work? If not, your I-PAC may not be accepting the programming or remembering the settings. Is the MAME/ALT jumper set to ALT?
If this doesn't yield a solution, I recommend E-mailing Andy Warne. He should be able to help.