It does not seem like this ever got resolved on this thread and I have the same problem.

I have 2 'parent' credit card accounts on QBO that are linked to my bank.  For some reason, it only pays the main credit card on the account setup with the bank.  So I show a negative amount on 1 credit card of over $1,000, but the same amount on the positive side on the other credit card.  Together it's a wash, but I would prefer it to be zereod out on one card and accurate on the other.

This chain never solved the problem - it sounds like this is something QBO just can't handle?