Oh yes! My hotel used to price all rooms the same by the number of beds, and the worst rooms (on the wings not facing the river or the few odd rooms that don't have balconies) were saved for last when we had to use them. Now, they are offered at a lower price, and are usually taken by people using third-party billing sites like Expedia who blindly click on the lowest price then become upset when they realize what they got, and we can't change the deal because they didn't pay us in the first place.
The thing about these third-party sites is they generate much less revenue, so it was decided that we wouldn't give daily breakfast discount coupons for our restaurant to those who don't book directly with us. This has caused some problems, but it's also caused some of our guests to become happy regulars that book directly even if we have to match their rates.
There is also the fact that Internet prepaid rooms are extra work to prepare, and since they started allowing same-day bookings, often with "I just made the reservation five minutes ago, isn't it here yet?" it must be said that these services are disliked by us front desk staffers who would prefer people just call or walk in. We can't simply check repeat guests in from history—we (and they) have to enter their personal info from scratch every single time. There is also the chance of making mistakes like charging their personal card the full amount of the room since they were already charged by the third party before coming in, and as the night auditor, it gives me more types of mistakes to be aware of and hunt for.
Needless to say, it wouldn't surprise me if Expedia and Priceline users are unintentionally treated like second-class citizens because of all the extra work they create. I try to treat everyone the same, but I still feel that twinge when someone comes in saying they have a reservation, and I had already checked in the last arrival of the night.