Similar, I think. Your issue is like you received 10 individual check for $100 in 10 payments?
My issue was customer paid in full let's say $100 but in 2 individual check. So we had to apply that 2 checks to one invoice in Lock box.
So we had issue that was not clearing the last balanced amount. But after the lock box file has been updated it has been corrected.
But if customer pay partial/residual payment then the balance should be open /on account for later payment.
Thanks