You are in luck. I have been dealing with Milkshape's UV mapping glitch for over a year and quit my projects due to it. I was working on porting Quake3Arena weapons and pickups to UT even tho it doesn't support shaders I was gonna try my best to make it look alike as much as possible. The biggest problem I had was the UV mapping getting moved whenever I exported to .3d or .psk and was not able to find a fix that will export it correctly directly from Milkshape. Luckily, I went off and gave it another try and finally figured a way how to reverse the misalignment of the skins in the meshes. So, here's how I do it...
--Since I Import from .MD3 files which supports multiple groups/materials, I moved the texture to where it gets when it glitches.
--Once you've done that, export the model to .MD3 and start a new session.
--Import that model you just exported and you'll see that it will import with the misalignment you did before in order to reverse it.
--Now, just to try if the UV mapping will get reversed, export it to the format that was getting screwed up and see if the skin aligned properly this time.
This process takes a bit of work to get the uv map to align correctly but it does work and the skin doesnt go out of bound when you export it to the UT model formats. Also, for some reason, some of the simple shapes don't screw up the uv mapping so check which materials are the ones going off first.
When I use the Texture Coordinate Editor in Milkshape the average offset I add is about 0.004/0.004 before I export it to the MD3 format to reverse it from the second import. Oh, and make sure to have the original model and the one with the UV map moved in case you need to repeat it again.
Well, I hope this helps and if it wasn't clear enough let me know where you got confused or didn't understand.
