I want to jump in on this, because what just happened to one of my clients might be what is causing your problem. 

Under Account and Settings - Sales Tab - there is a new "feature" called "Your customer pays the fee"

It is not rolled out to all my clients and we weren't given notice. My client ended up having her invoice paid via QBO payments, which we haven't used in literally years. We then had to reverse it. Monday morning I now get to contact more clients, it was not rolled out to all of them. 

To the poster - if you are continuing to have problems, check to see if that box shows in your system and de-select it. That single check box allowed a payment to come through QBO, NOT my client's payment method-for very good reason.

To intuit - this is one of the most inappropriate updates you have ever put on my clients. It is damaging to their professionalism and how they conduct business. If end users have your payment processor turned off, it is for a very good reason, and for you to default enable something like this is unbelievable.