Same thing has happened to me at ORD. They assured me that it wasn't possible for them to move the car from the return area without it being scanned. Well, apparently it did, however they scan the car (or are supposed to) every time it's moved. So they were able to see that the car was moved later that day.

Similarly to others, I wasn't able to get anywhere with the central customer service and ORD never answered their phone. Luckily, I just stopped back in the next Monday morning and had them finish the paperwork then. IDK how I would have got them to close it out if I didn't keep coming back to the same place though.