Is there any reason that this should be happening? Even If I use generic skins that arein the game already I get the stormtrooper in cutscenes.
Stormtrooper seems to be the general fallback player model for the game. If you try to insert an NPC that doesn't exists, you get an ST. If you make a mistake entering information in NPC_spawner, you may get an ST. If your NPC files are faulty, you may get an ST. Perhaps if you have conflicting pk3s in your base, it could lead to an ST. Or perhaps your game installation is just haunted, and a spirit of a dead stormtrooper is trying to tell you something by appearing in all your cinematics...
Id say its the perhaps, bu then again i once deleted my curser from the pk3. (was bored) and it look like a BIG white block. I think you sould re-install