Hmm, seems like I was having issues with the deleted invoice posting to QB correctly. I can't remember exactly what it was but I think it might have been been that when I looked at it in Quickbooks, something in the lineitems wasn't right. I think I was trying to edit it in Method but it wouldn't update in QBO so I eventually deleted it. Probably deleted it in QBO. That may have been the issue.
Just for clarification and future reference, you went in to the received payment, unchecked the "Auto Apply Payments?" and then selected the invoice from the list? Is that correct?