I get the feeling that many, many, many of these scrolling sites were only tested with two-finger scrolling on an Apple laptop touchpad. They often feel extremely awkward with a regular scroll wheel.
I use an Apple trackpad with two-finger scrolling for 70% of my web browsing. I have yet to encounter one of these scrolling sites that didn't feel extremely awkward on it. Maybe the target audience is iPad users? I feel like the behavior might make sense on a tablet.