Have not read further to see if you got this resolved but I called AT&T and paid just my last installment fee needed to upgrade. I logged out of my account and back in and it now shows I'm eligible to upgrade with no additional fees.
I will drop my phone off at an AT&T store (recommended by the rep I spoke with) as opposed to mailing it back in.
So if you are still showing online that you have an installment left, call and make payment over the phone. They can apply it to that specific line item to make you upgrade eligible.