Payment is showing unapplied with a balance of $0 remaining

Once a payment has been fully applied to a charge, the status of the payment will show Fully Applied. 
Contact Support and reference this article. 

Alternative Solution:
  1. Unapply all the payments associated with the invoice.
  2. Note: Make note of the check numbers.
  3. Reapply all the payments to the invoice.
 

Environment

 7.82.104, patch 21

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