I had the same with Bromley and an FPN, rejected the first time and told a second appeal was only "allowed" one the notice to keeper had been issued, and discounted period expired.
Needless to say I bombarded Bromley Council, Parking Services, Civic Centre etc with emails until I received a reply.
Amazingly the FPN was at that point cancelled. Not due to the strength of my appeal, but due to a "clerical error". Which I can only assume was sending me a letter rejecting my appeal in the first place.
They are a law unto their own, and occasionally need reminding they are a service and not just there to issue penalties, ignore appeals, and take your money.
Silly question, but does your bank account show the payment having gone out? Did you get the emails with your payment receipt and transaction ID?