Sure sounds like someone dropped the ball on this one. Previously, if I had a cabin on hold for 48 hours, no deposit required, but after the 2 days you either loose the cabin or put a deposit on it, wondering why they would require a deposit for a 2 day hold.
I'd call the travel agency up and inquire, they should refund the deposit. I know sometimes they can sure take you money quickly, but take a billing cycle or 2 to return it back, hopefully thats the case, but check it out more.
If nothing happens, file a complaint with your credit card and fight for the return of the deposit.