Sheryl, sometimes this happens because the 800 numbers that you call for hotels, are not that hotel's employees, but a separate company that has a contract with the hotel to book rooms. That booking company has a certain number of rooms that are theirs to sell.
For example, a hotel may have 200 rooms and of those 200, 50 are allocated to XYZ Booking Company to sell. The hotel reservations staff already have confirmed reservations with credit card guarantees for 150 rooms. In essence, they are sold out. However, if you call the 800 number of XYZ Booking Co. they may still have rooms and so you can get a reservation through them.
That's just how the system works, but at least you found the way around it.
Also, sometimes the XYZ Booking Co. has the rooms at a certain rate, but if you call the hotel directly, sometimes you can get a lower rate. Go figure. These are just a few of the vagaries of the hotel business.