I did a test where i remove the HUD and the HUD Glass. My Weapon Control Panel is transparent and it also showed no ammo (0000). So there is not a problem with the CSWeapon.xml file. ;)

The [Window Titles] looked like this:

[Window Titles]
Window00=Main Panel
Window01=Weapon Control Panel
Window02=Radio Stack
Window03=GPS
Window04=IFR Panel
Window05=Landing View
Window06=Mini Panel

And the result was this:
http://i669.photobucket.com/albums/vv58/Markoz958/2012-11-1_13-23-38-361.jpg


Once I put the 2D HUD back in the panel.cfg, it returned to normal with ammo (200). So it is a case of you must have the HUD included or it won't work. What I did was make the HUD as the last Window entry. I was testing with the C172, and so I put them in this order:

[Window Titles]
Window00=Main Panel
Window01=Weapon Control Panel
Window02=Radio Stack
Window03=GPS
Window04=IFR Panel
Window05=Landing View
Window06=Mini Panel
Window07=HUD