To elaborate on this point: when you run a level from JCS.exe (as in, by using "save and run") you it will always launch Jazz2.exe. Therefore, if your copy of JJ2+ is called Jazz2+.exe, JCS will not run it.

If so, just rename the JJ2+ exe to "Jazz2.exe" and backup the original. That way, JCS will always launch JJ2+. There's no harm doing this, and in fact, you probably won't ever want to run the unpatched JJ2 anyway.