Well if you have the original cd then no problem. I just meant that the MotS patch has to use the original EXE file for the game (and therefore you can't use any "no cd" cracks or patches, because those alter the EXE and will make the patch not work).
Use the "Unofficial MotS Patch" from the JKHUB.net site (I believe the sub-site on it is called "Unofficial JK Patch" project.
You apply that patch FIRST and then take the renamed (from gob to goo) JKE (latest version) and it will work.
If it still doesn't, please describe STEP BY STEP exactly how you are installing it, and where MotS is installed on your hard drive and we'll try to help!
Perhaps you should try it in JK first to make sure it's working properly (the JK unofficial patch + JKE). THEN try it in MotS...