I just figured out why 2 of my customers E-Invoice payments are not being applied to the invoices.  When they pay they use the owners of the cards name and not the business name.  Since I do not have that in the customer info, it does not recognize who that customer by way of Company name and it does not apply it to the invoice.  Voila, I hope that is it.  I am putting the name on the card that they use to pay the E-invoice into my customers info to see if that solves the problem.  It only happens with two customers and both of them do the same thing.