OK, here's what I found. The MAME jumper set. buttons 5 and up on players 3 and 4 do not function. The WinIPAC program also doesn't register they're being pressed. When that happened I assumed it was the ipac or a wiring issue. I set the config to ALT and reprogramed it with the default mame settings + players 3/4 buttons 5-8 configed. Which appeared to fix the problem. However I also noted in the WinIPAC program if you do not have the same config loaded or something with those buttons defined it still does not register a button push even in debug mode. They buttons still function but the program doesn't appear to notice they do.
Eric