First, thank you for posting your results, I have not tried VS duck hunt, will try that in the morning. I have a few questions if i may.
1. In your mame.ini do you have lightgun set to mouse? Do you have mouse set to 1? Because if i understand this right the script just moves the mouse position around, so just enabling the mouse should work. However now that i think about it, when I remapped inputs for alien3 mine showed up as gun1. But I think area51 showed it as mouse... hmm I will look into that in the morning.
I got duck hunt to work. I set mouse to 1, lightgun to 1, and joystick to 1. Just having the mouse set to one does not work. If it did we would be in business. That is what we want. Mine shows up as gun1 as well.
2. What were you using for an IR source? With the last posted script mine hasn't jumped around except for when the batteries in my wireless sensor bar were running low, then it jumped like crazy.
This is resolved. My IR source for the record is the Nyko wireless one. Not sure why it wa jumping before but it works now.
3. The weird firing symptoms I dont really have many ideas for, except: Try shutting down glovepie and reopening and running the script again, I have had it flake out a few times, but it was always the tracking that did not work at all, the buttons were always rock steady. The delayed shots could be the computer not being able to handle the game and glovepie at the same time.
This was resolved. Stupid mistake by me. I did not have the joystick set to 1 and I actually mapped the fire button to gun movement.

4. What system specs and OS are you running?
Athlon 64 X2 Duo 2.21 ghz, 2gigs of RAM, Windows XP SP2. I should be good for duck hunt

5. When you remapped your fire button which joystick did it show up as? Just idle curiosity because mine will show up as different joysticks from time to time.
Joy1 I will check and see if it moves around.
So I also noticed a few other things. I read through the Glovepie documents. It says to control more then 1 mouse use "mouse1", "mouse2", instead of just mouse. My thought process is if we connected 2 mice (ie trackball and regular) we could control movement of each and therefore we could map them seperatly in mame. Still looking into it. But until we can get Mame to recognize it as a mouse we are out of luck.
Also, I could not get the buttons to work without PPjoy either.
And one last thing, I went to the midnight showing of Ironman last night and I highly recomend it.
