Did the statement(s) show a required payment?
That is exactly what I would check - if your credits from the refund are bigger than the minimum payment, the site would show NO minimum payment is required at this time.
In fact when the credits fully cover the outstanding bal on prev statement, the site would show NO outstanding balance from previous statement. Besides,unless you have current charges, Chase system would not even allow you to pay from its own site except being pushed from another bank.