Within Mame, press TAB to enter the menu and ensure fire button 1 for the second gun is mapped to the appropriate device. The other day, my gun 1 didn't want to fire but it would track the cursor properly. When I went into the mame setup, I noticed that the tracking worked because it was set to "lightgun 1" but the fire buttons were mapped to mouse 5, when it should have been mouse 4. I remapped the button 1 again and it worked fine.
The reason for this is because I always disconnect the USB hub, so as to preserve the life of the guns/LED's. Even though I reconnected them in the same USB hub, for some reason the PC allocated Gun 1 to a different "mouse" number.
Whatever the case, it worked for me, so check it out, I have a feeling that's your problem.