Hi Ken,
Could you enable MethodSupport on your account and email me the Company Account name? If you could also indicate which invoices and receive payments this applies to that would be great.
I think the root of the cause is the invoices and not the receive payment. Are you seeing this error in the Resolve Conflicts screen? I was able to replicate this by not syncing over an invoice then trying to receive a payment and applying it to the invoice that didn't sync. However, you're saying that the invoices did in fact sync over, correct?
To enable MethodSupport, go to Customize > Users and check the checkbox next to the MethodSupport user at the bottom of the User list.
- Adam