It could be the IPAC programming, or it could be what is assigned in MAME.
Hard to pinpoint what the issue is without more info. So here are some questions for you...
1) Is every control exit the game, or just when you hit right on the joystick? What do the other controls do?
2) Are you using the standard MAME keysets, or did you program custom sets?
3) Is this the IPAC VE? The VE doesn't keep the custom programming stored on the IPAC, so if you turn of the machine you loose your custom programming, and it has to be reloaded.
4) Load up a text editor like notepad and see what you get when you use the controls? Do they correspond to what is setup in MAME?