I am having this same issue with one of my clients!  Have always had credit card option turned off, all the sudden client gets an email with credit card pay as an option & in spite of escalating to QBO supervisor, they are denying the credit, as well as denying an offset on his monthly subscription fees.

This has to be illegal and if I don't get resolution (on the phone again), I will be seeking legal input or possibly seeing if I can get attention of local news station - I am convinced this is a programming issue on QBO side, likely in line with their new invoice changes.

So frustrating!!