Once I get into the duck calibration screen none of the buttons on either of the controllers (normal in port 1 and gun in 2,3, or 4) work in 480p, 720p modes. However, I did just try your emu in 480i and had similar luck as I did in Xports emu's (being that it gets through the calibration settings at least, but it still isn't aimming correctly). I did just try a couple bits of trail and error and found out that 1080i does also indeed work though has the same symptoms of 480i. Maybe a progressive scan issue.
However just to document exactly what I saw, after calibrating both 480i and 1080i the Y axis worked perfectly. Odd thing was that when I aimmed steady at the screen (anywhere on it), while the Y axis stayed the same, the X axis in 480i mode went from the right side of the screen to the left side while 1080i went from left to right. Fairly smoothly I might add. This pattern repeated as long as I aimmed my gun steady. When I moved it up or down a bit the curson started at its respective side of the screen and started the left to right (1080i) / right to left (480i) all over again.
Anyway, probably a bit to wordy, but that is what is happening

I don't have a normal 480i TV that I can test as of right now, so the TV being the problem still isn't out of the question.
TV / Xbox specs for referance:
Xbox : version 1.1
Softmodded with Krayzie's Ndure ver. 1.1.1
Hard Drive upgraded (200 gig)
XBMC 2.0.0 T3CH (FAT version) as main dashboard
TV : Sony 34" XBR960
Xbox hooked through Component AV pack running 720p 95% of the time.
Hope this helps, and I will be more then willing to test any kind of fixes as well as any other 720p/1080i issues if nessisary.
Thanks!
Sp3eD
What emu's does it work flawlessly on? I have only tried ZsnexBox and mednafenxNES version 8. Did yours work with Xsnes9X?
What does it say on the screen when you point the lightgun at it in 720p? Does it say it's calibrated for this mode? Does it display X, Y coordinates in the lower left corner?
Has anyone else out there gotten a lightgun to work in 720p or 1080i? No one has said anything about Lightgun support in HD modes, so I don't know if it is a lightguun, bios, Xbox version, TV, code, or HD issue.
The only thing I'd be able to do would be to fix it if it's a code issue. If it's anything else, then there would be nothing I could do. I just know that my Lightgun (Madkatz) works on a 480i TV using a 1.6 Softmodded Xbox.