If you don't have the alpha channel in the texture anymore and if it still render transparent in the game, then I'm afraid that Gscc (doctor of funk) is right and that it comes from the trimesh model of the window.
Euhm, Its not difficult to add an alpha channel, its like one click on a button...
Some textures Kotor don't have one, but like said above its one click away.
Else make a .TXI named tel_wn03.txi and its should contain this:
envmaptexture CM_Baremetal
Its a Notepad file, buts saved as AllFiles, set to ANSI.
You just need to add the .txi
Check it out if the window turn "black" metallic.
EDIT: Take a look, I did a quick test myself.
1) Just made a silly TXI with the metal shine effect in it.
http://i116.photobucket.com/albums/o34/slazzir/K2_Zever5.jpg)
Windows where still slightly transparent.
2) Here I used another texture to replace the windows texture, though I made sure to make the Alpha Channel 100% white, which means 0 effects.
Just to be sure I left in the previous made TXI.
http://i116.photobucket.com/albums/o34/slazzir/K2_Zever.jpg)
All windows turned to solid steel and there was 0 shine effect :p