To fix this im just using the elegant bastilla skin. This skin does not have the shoulder pad thing with it and so far it is not transparent. Alternatively instead of trying to see what is wrong, maybe create a seperate txi file for bastilla instead.
Edit/update- Ok well I went into photoshop to see if there was an alpha channel that caused the transparency and it seems like any bastila skin that has this will make it transparent. The elegant bastilla skin I am using doesn't have a alpha channel which is why it isn't transparent. So I am going to assume that the original skin has some kind of alpha channel that causes this and because there is no txi file it makes it transparent. That or a txi file included with these textures has changed one of the original txi files in game used for bastila's skin which is why this happens. Problem solved sorta...lol(Well the first step to this anyway).
Edit- Yup, I was right there was an alpha channel that was somehow changed with in this projects development. The only question is what kind of txi did this particular skin use? To fix her skin I got the original skin and deleted the alpha channel therefore eliminating any conflicting txi file. What I suggest is finding the original txi file that her skin used and adding it to the plc files. Im not too familiar with these textures which is why I haven't attempted to tackle this myself(That and I forgot how to use the functions of kotor tool from my long break from modding).
Edit- Well it seems its not just bastila that this affects, you wouldn't notice it but npc's like certain black vulkers and a few other have some sort of small transparency in one part or another(I really had to look to see this). Its very interesting, not sure what it could be.
final edit - Actually its not your fault Xar, its something that bioware messed up on.
This thread explained to me why this occurred, even when I had no mods on. The fix I suggested still works but its something that bioware forgot to adress. In short, your mod doesn't cause this, its something hardcoded in the game and a problem windows 7 users like myself have. I have the most up to date version(kotor collection) and its a shame that they could not fix these problems to start with.