The colours might be messed up, because your textured background's colours probably are very much alike the colours elsewhere in the set.

JCS messes up the files to make them as small as possible. Which means that Jazz probably is now using colours outside the texture palette for the textured background. (I hope I'm being clear, you can't explain a lot with my knowledge of English :P)

Try making a textured background with colours quite different from then rest of the set.