I know most car rentals will not rent you a car unless you lay down your credit card or give a cash deposit. This is in case you do something to the car, like leave it real dirty, ash burns in the seat, flat tires missing hardware, empty gas tank when you return it ect...

It sounds to me like you may have been billed twice. That is why you are supposed to tell them to rip up the CREDIT TRANSACTION in front of your face after you pay them with cash, or check. You must have paid with a check and walked away without telling them you had paid by credit, and if they told you that they would take care of it, you should have told them to GIVE YOU THAT CREDIT transaction. They have to give it to you. I don't see any foul play here. You don't have to pay what you have paid all ready with your proof. Just send a copy of your paid statements, receipts to your credit card company. You may want to call the rental car place to clarify. One last question. Did your check bounce?