So, I've created a new level using 3dsmax. It works fine, it loads and the walkmesh fits. The problem is that some of the textures seem to have invisible gaps in them :

http://img826.imageshack.us/img826/4073/swkotor2201011251200026.jpg)

There are meant to be two tall pillars there with runes etched into the side. The runes are showing, but the actual pillars are not. The applied texture looks like this :

http://img338.imageshack.us/img338/1201/nihtr05copy.jpg)

Can anyone tell me what I'm doing wrong and hopefully how to fix it?

have you checked the alpha 1 channel of your pillar's texture? If there is any black in there, the model might be applying the game's default shader (which is transparency).

Thanks. I just deleted the alpha 1 channel and everything shows up fine now.

Was this a sensible way to do it, or will deleting it come back to haunt me later?

No, it shouldn't come back to haunt you.