First of all, welcome to FlyerTalk!

Yes, you are still responsible for the late fees and other charges because of non-payment. Your original charge was reversed (read refunded). The charge-refund and credit card balance due are independent of each other in this case as from what I understand, there was significant lag between these events, i.e., they were not within the same billing cycle.

The only thing I can think of is if you complain to the merchant about the delay in processing your refund, they might offer you something like a small amount of gift card or credit as an apology.

I am sorry to say but there isn't much that you could do as I foresee. Good luck! ^