What difference does it make what number the gun is? As long as it works, it should be fine.
Well for a game like Point Blank 2 for example the cursor or cross-hair on screen shows up as red (which is player ones color) even while playing as second player (blue player). Not a huge deal but just not perfect is all. I was just hoping there was a fix..but I suppose unless I were to unplug the mouse its not going to happen.
You are mixing some things...
You had the mouse connected when you plug the Aimtrak. So For Windows, there is two "pointer" devices. First, the last new device plugged: The Aimtrak; second: the mouse. MAME inverts this list, so in MAME, the mouse is the pointer device 1 and the Aimtrak is the second one. It not depends on which device you assigned to the gun in the Aimtrak Utility.
And remember that you can remap all the keys and axes in MAME, so a Gun 2 can be used to play with player 1.
About the color...This is another (completely different) question:
You can change the cursor (shape and color) in MAME for each lightgun game.
Press Tab and you will see a Crosshair menu. You can download some crosshairs to match the color of the games (remember those games not used crosshair in the real thing) and more info here:
http://mrdo.mameworld.info/mame_artwork_supp.htmlAll those things are explained in the guide Andy Will release soon.