Hi Henry,
I've been trying to learn as much as I can about Face ID and its repairs and related information, and to the best of my knowledge the rear facing cameras are not tied to the Face ID system and can be replaced at will without issue. In actuality, the front camera isn't tied to the logic board either, but is harder to replace by itself since it's mounted in that metal frame with the rest of the front camera assembly components, the dot matrix projector and the IR camera (both of which are paired to the motherboard).
I actually had a similar problem with the cameras not working, but in my case it turned out to be the IR camera that was causing the issue. Replacing the IR camera restored the function of the other two cameras, but of course that cost me Face ID.
So yeah, I don't have an answer as to what's up with the JCID software, but there are a lot of guides, techniques and troubleshooting information available for the iPhone X that you can look through to see if there's an answer.
I have the QianLi iCopy device myself, so I'm not up to date on the JC product, but there are a few people on here who do have the JC programmer and hopefully they can chip in.