Hi u-rebelscum
Which version of mame32/mameUI are you using?
Assuming it's semi recent, make sure you are mapping the AD Stick Analog items, and NOT the AD Stick Inc/Dec items. For more details, follow the instructions here (even though it's written for actlabs).
I´m using mame32 V 0.123 in Windows XP, I make another attempt yesterday and found something interesting, I select the "lightgun" games in mame but alien3 and operation thunderbolt are not present, then select "trackball" games and there thy were, so I change all the mame default control to lightgun and operation thunderbolt works great, but alien 3 still not.
Also change the cfg file of alien3 ad stick for player1 with a text editor and still the same, I change the analog control, NOT the Inc/Dec.
Sounds like the gun is shorting somewhere when it senses the LEDs. This could be anywhere from the optical sensor to the chips to the power convertor in the gun, to the USB cable, to the USB port in the computer. Is recoil plugged in? This was the first to go in one of my LCD guns; try leaving the recoil power unplugged (even though I doubt this is the problem, it's the easiest to test).
Also plug again the gun (the bad one) and now windows pop a USB failure, telling the item had fail and is not recognized by windows (I will post the exact text when I get home), I think the gun is death, but I will plug it to my brother's PC just to be sure.
thanks again u-rebelscum.