I can see how this rounding issue affects the accuracy of your data, @freddefesc.
At the moment, QuickBooks Desktop rounds up to two decimal places only that sometimes causes penny differences. As a workaround, you can update or enter the payment amount manually to prevent this.
I'd also like to let you know that our developers are constantly uncovering and considering new ways to improve the program. To be updated with our latest news and enhancements, you can visit our QuickBooksBlog site.
Please let me know if you have any other issues or concerns. I want to make sure everything is taken care of for you. Have a good one.