Hi mvi,
I have some questions in regards to this issue:
1. Are there any conflicts in Method? You have two ways of finding this information:
a) Select QuickBooks from the tab group dropdown in the top right and then go to QuickBooks > Resolve Conflicts
b) In the CRM tab group, go to QuickBooks > Resolve Conflicts
2. Have you tried to delete and add the payment in method and is this happening for a particular customer/invoice?
Ronen