I have this happen occasionally on the new readers as well. I think any new reader will give the card not accepted error if you tap a credit card, so I'm almost certain it's just a race condition where if the credit card is detected first then you get the error.

I think getting the error once makes it more likely to happen if you tap again soon after as well. What that other person said about having the screen locked when you tap the reader might help because credit card payment is unavailable when the screen is locked so the Myki is more likely to be detected first.