You might want to steer clear of light guns altogether then as there is much dinking around in MAME to get them calibrated and working after the hardware installation is done. You've got to calibrate the gun, set options in MAME, and remember to do the native, in-game calibration for each game IF it is required. I haven't gone through this yet, but it sounds like it aint easy to get guns going on a MAME cab, especially if your expecting to hook guns up and start shooting.
I think this guy had the windows cal done right, but the ingame cal wasn't ever done. When he shoots onscreen, the aimtrak would tell MAME he was onscreen, but since he never did the ingame cal, it doesn't know where to put the shot. If he shoots offscreen, the aimtrak senses it and tells MAME and all is ok. I'm just guessing here as to what his problem is, but you have to expect to deal with these sorts of non-intuitive issues. It's just the nature of using hardware that's a level away from the emulation.