There might be some wear that might be causing that, too. Since the sliders are plastic, depending on which key the parts were pulled from/put into, they wear on the slider might be a little different. The new "T" key might feel a little different than an old one, or it might feel different than the "Q," for example. I have never, personally felt any difference in swapping Cherry guts other than trading a less worn key for a more worn key. The only other thing might be if you swapped between a Cherry-manufactured and a non-Cherry 'board (say, a Filco). Apparently, they make switches for Cherry 'boards in another factory/assembly line than they do for non-Cherry 'boards (there is an early thread here that discusses this). There might be some minor manufacturing difference that could explain the different feel.
Actually, I had individual switches that I got from Digikey, and I've played around with the three I got, a blue, a "clear", and a black.
Having lost a spring inside a keyboard when pulling a key on my Cherry keyboard, I decided to swap out the brown slider for my white one, and comparing it to the one other white switch that came with the keyboard, it felt different.
Probably, it was just less lubricant on the slider, as the one I transplanted doesn't seem as smooth as the original.
I also replaced the gray switch for the spacebar with a black slider and spring, which actually feels a lot nicer, I'm almost thinking about making the rest of the modifier keys linear.
So, maybe there are differences, maybe there aren't, but considering the only thing that matters is how it feels to you, I guess it doesn't matter whether the leafs are identical or not.