i've had trouble finding a keyset that works with everything. i use an ipac 4 in my cabinet and have long since abandoned the default keyset, which is crap. i keep p1 joystick as the arrow keys, p1b1 as enter and then just try to use regular keys for everything else, no shift/alt/ stupid special keys. for the most part this works for most things. but there are always things that do not work.
what i ended up doing is using the winipac program to make custom keysets for the apps that don't work right, then use batch files to load the proper keyset into the ipac, launch the game, then when it exits, set it back to my default keyset.