You could try the 1.01 patch available from LEC's website.
You could try uncheck (or checking if that doesn't work) the box that is labelled "backbuffer in system memory" in the display menu.
If you then check the 3D Accelerated box and you still aren't in 3D mode, then I either suspect you have an older version of directX (you need at least 5.0 for JK/MOTS), or your video card isn't connected properly.
There are some video cards/chipsets that JK doesn't support very well, but you should at least be able to use 3D mode, even if it looks crappy.
Get the latest DirectX
Get the latest drivers for your video card
Get the JK 1.01 patch
Try the backbuffer thing
If none of that works, try Yoda's Help Desk on the LEC website. www.lucasarts.com