Alright, so this is strange. When I had the HUD where it was originally, the images appeared as normal, but not moved into the right places. When I put the .pk3 into my JA+ folder with "zzz" as a prefix, there was no HUD when I loaded JKA. Perhaps I'm inputting the wrong coordinates or something? I just assume since the HUD is a 640x480 "box", the coordinates and sizes that Adobe Fireworks give me would be correct
Basically 640x480 HUD is not a "box", because it's only 2 dimensional. Btw I'd still advise you, share your pk3 with us, that would give us a chance to figure out, what did you do in your ui file.
Do you have a vm folder in your pk3? or any qvm files?
JA doesn't use QVMs, but DLLs. The HUD is controlled by a ***.menu file though.