Well, not sure what I did but everything appears to be working fine now. I did so much that its hard to say what actually fixed my issues but I will list them below. Hopefully they can help people in the future:
- In the aimtrak configuration utility, reprogram the guns to different IDs ( conflict with my mouse, maybe this fixed the double button press showing up in config menu).
- Unplug both guns and plug one in, recalibrate it in aimtrak. Repeat for the second gun.
- In the mame directory clear the cfg, nvram, and dif folders
- Remap the guns in the mame config menu (TAB).
- Some games require you to do additional setup and calibration within the games service menu (F2)
- If you are having trouble mapping the aimtrak's side buttons, joystick must be set to 1 under core input options.
- Below are my mame.ini settings in regards to conrols and light guns:
#
# CORE INPUT OPTIONS
#
coin_lockout 0
ctrlr
mouse 1
joystick 1
lightgun 1
multikeyboard 0
multimouse 1
steadykey 0
offscreen_reload 1
joystick_map auto
joystick_deadzone 0.3
joystick_saturation 0.85
natural 0
joystick_contradictory 0
coin_impulse 0
#
# CORE INPUT AUTOMATIC ENABLE OPTIONS
#
paddle_device none
adstick_device lightgun
pedal_device none
dial_device none
trackball_device mouse
lightgun_device lightgun
positional_device keyboard
mouse_device mouse
#
# INPUT DEVICE OPTIONS
#
hide_cursor 1
dual_lightgun 0
joystick_id_1 0
joystick_id_2 1
joystick_id_3 2
joystick_id_4 3
joystick_id_5 4
joystick_id_6 5
joystick_id_7 6
joystick_id_8 7