Hi,

I have a similar issue but the description you gave did not fix my issue. I have a few clients who pay me directly through the QuickBooks online payment system, so the payments come in twice, once through QuickBooks and once through my bank feed. They both are reflected as payments. One gets automatically applied to the invoice, but the other remains in unapplied funds. I have been excluding these from the register in order to have them appear only once, however, on the customer summary, they show a credit balance due to these transactions.

Can you help me resolve this? 

Thank you,

Julie