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It was paid directly to them. I provided them with the receipt & confirmation number THEY gave me when we paid, that's when they realized it was a problem. They told me that there was some glitch in their computer system that kept the pre-paids from appearing (yeah right) I honestly think the guy at the front desk didn't know what he was doing when I checked in. He had so many problems just getting me checked in. I'm sure others that checked in that day are having the same problem.
If the hotel has acknowledged that there is an issue and is working on it, Im not sure how far you're going to get with a dispute. Your card company will probably ask you (if they havent already), if/how you've tried to resolve it with the hotel. And if you tell them the hotel is working on it, they'll probably ask you to wait until the hotel is finished trying to refund you before going further (and if you say the hotel isn't trying to resolve it, when they contact the hotel about the dispute, the hotel will probably tell them that theyre trying to refund you...so its best to just be up front about what has transpired thus far).
I dont know how much the charges are for, but unless you booked a $10,000 suite, the increased utilization is probably not going to have that big of an effect on your score. And when the util goes back down on the next statement, your score will recover (if it even goes down at all in the first place). If you're super worried about it, just pay it now, and then you'll get a refund against charges on your next statement.