I'd try a game other than Area51 or Maximum Force for testing.
Those games gave me fits when adding the second gun.
Anyways, I have two old ray-gun style Act Labs TV Light guns that use S-Video.
Both guns work like mice and they both behave the same in the windows environment.
Trigger is the left mouse button, button on the side of the gun is the right mouse button.
The pointer will move to where I shoot. If I shoot at an icon, it will highlight it, but it doesn't register
the clicks fast enough to double click to open it. If I press the button on the side of the gun,
the right click menu will open up. Then if I pull the trigger while pointing at "open", the program will launch.
It works the same with either gun.
Under Devices, they both show up under Human Input Devices and say "ACT LABS USB TV LIGHT GUN" after the location.
They also show up under mice, but show up as generic microsoft usb mice.
I also have the trackball in the x-arcade that shows up as a mouse and occasionally plug in another mouse.
These things have never interfered with the guns.
The only other thing I can think of is that I don't have the troubleshooter installed (but I was thinking of installing it).
Keep me updated!