I'm not entirely sure your particular issue is related to mod incompatibility. I remember, back when TSL worked on my computer - stupid incompatible Intel cards and Windows 7 - a lot of animations did not work. Some examples are Nihilus and Bao-Dur. At one point, Darth Traya's lightsabers also stopped working for me. (Every turn, damage was dealt to my character, though I did not see any animations. Just my opponent standing there.) Note that all of these issues were without mods and happened on both the Xbox and PC for me.
This can possibly be an issue with the code - I'm not too sure. I remember having the same issue in KotOR 1 at times - the solution to which was to simply restart the game. The solution is not so simple for KotOR 2. In fact, I don't remember finding one. :/