Cartridge BASIC is definitely compatible with Jrconfig, so that is not the problem.
Cartridge BASIC has some known bugs when running on a machine with extra memory. I remember that on my PCjr with the Microsoft Booster they included a program called jrbasic.com that would do some sort of addressing fixup to allow Cartridge BASIC to work. JrBasic checks for the MS Booster, so unless you have one that is not going to work.
Then again, there was another version that IBM had on it's BBS. There is a mirror copy here:
http://john.ccac.rwth-aachen.de:8000/ft ... _specific/Look for jrbasic.zip. And if it works, post here to let me know and I'll post it.