None of what you encountered with Kayak is really abnormal. Hotels change names all the time, and the 2nd and 3rd party booking sites are slow to keep up.
By fax is how hotels receive your reservations, and it does take a while for the 2nd and 3rd parties to send them, and then it takes a while for the hotel to notice the fax, and get them entered.
The mark up should never have been shown to you. The mark up is high, because it basically is free advertising for the hotel. Expedia mark up is mind numbing.
I dont understand what the problem is, as you were booked into the same hotel you thought you were booking, it just had a different name. Maybe you thought you were going to get points?