I am not positive on how to fix this... it is a strange problem cause it does not happen to me at all... both my JK and MotS work flawlessly
I will do some research and try and find a fix for you guys...
in the mean time try getting the unoffical patch for JK and MotS over at www.jkhub.net
and see if that helps... go under Projects in the top corner and look for Unofficial Patches or something like that its by ZeqMacaw, the unofficial patches fix a lot of things for JK and MotS like texture limits ect ect. See if that helps... if that does not I will keep looking for a fix