I use Merchant Services for running credit cards, and I recently found 2 accounts that I ran credit cards on that applied less to account for what card was ran for, for example, I ran 1 card for $550, only applied $350, other was $800, applied $730.

Thanks for bringing this to our attention, @JT70. 

Every penny counts when running a business, and I'll make sure you get the right support available so you can get back to running your business flawlessly. 

To further check your account safely and find the root cause of this issue with your accounts, I recommend contacting our Merchant Support team, which is best at handling this kind of query. 

Let me know how else I can help you with QuickBooks Merchant by adding a comment below. I'm more than happy to lend a helping hand. Keep safe.