Did you ask for another room? Did your end up in an upgraded room or anything else that was special about your room (NS, King, etc)?

From your title I took it that you meant you were not allowed to check into your room for two hours.
From your post you said that you ran errands / had a beer and when you came back, three plus hours later the room was ready.
Did you take the meaning of what the clerk said, "I don't think it will be two hours." to mean that it would be MORE then two hours or LESS?

I would have taken it to mean that it would have been less then two hours.