I'll answer this question for you, @KenLee.

The ACH rate for QuickBooks Payments is still 1%, with a max of $10. In your situation, I suggest you contact our QuickBooks Payments support for further assistance. They can pull up your account info within a secure environment and investigate the transaction in question for you. See this article for the steps: Contact Payments or Point of Sale Support. Please take note of their operating hours, so you know when they're available.

I suggest you view this article: Find out when QuickBooks Payments deposits customer payments. It includes the steps on how you can check for payment issues. 

Post a reply if you have other questions about the rates in QuickBooks Payments. I'll be sure to get back to you. Enjoy the rest of the day!