I use Win2kPro. I didn't have to do anything special to play JK, it just plays. Don't install the version of DX found on the JK cd's, it's old and outdated. The game should still work fine. Apply the 1.01 patch and see if it helps any (probably not, but it's still a good idea).
If all else fails, go check out http://support.lucasarts.com
and see, they have a lot of solutions for the older games as well as new (just ignore their forums, I never get a useful response from them, sadly).