You're talking on mame, right? I looked at the source, and it looks like the trigger and pump are each listed with two inputs in the driver. One is the normal button 1 & 2, but the other is a IPT_SPECIAL type, an input that needs special code in mame. However in my quick skim, I couldn't find the special handling code.
Do other inputs work? If not, it could be a driver issue.