I had a similar problem once (an older version though); it was because some of the sounds were in .wav format and others .ogg so when you did a reinstall of the mod the batch files called actually deleted some of the sounds (as one .bat was set to run on uninstall). This isn't a TS thing so much to do with the way the tp2 structure interacts with WeiDU.
A solution is to uninstall the mod, then exit setup. Then go back and install it, again. i.e. don't just press [r] to reinstall...