Looks like this is an old issue. I know EXACTLY what you are referring to. I've recently upgraded to Mountain Lion from Snow Leopard, and I've been experiencing what I call the "snap to highlighted file" action. I've never had this happen on any of the older Mac OS since I've been using a Mac (20+ years). So I thought this was something new in 10.7.x and up.
It's excatly as you described. When you have one window open, and a file selected/highlighted (let's say near the bottom of the window...call it Y file.mp3), and another window open containing C file.mp3, I'll scroll to the very top of the window containing the Y file.mp3 (while that file is still highlighted). Now regardless of what the windows' arrangement are (Name, Date Modified, Kind, etc...), when I copy the C file.mp3 file from the second window, to the first window containing Y file.mp3, which is scrolled to the very top, the window will automatically scroll down to the bottom of the window where the Y file.mp3 is highlighted. Another crazy "glitch" in Mountain Lion is, randomly (not all the time, but it should even happen in the first place) when you select to change a file name within any finder window, the name bar highlights for you to change the name, then all of a sudden, it gets deselected, and a few files down, that file's name bar automatically gets chosen for the edit. Without you ever selecting. The only thing I can think of that's consistent with these issues, is that all my windows are set for List View. I've always used List View from day one of using the Mac. Visually, it's easier for me to view and organize my files.
I've tried some of the tips mentioned, but none of them worked. I've posted this on other forums, and no one seems to have an idea why it happens, or how to fix it. The only thing I haven't done is a clean install of Mountain Lion. Don't have 2-3 days to spare for reinstalling everything from scratch. And really, updates should work pretty flawlessly in my opinion. Other than this and a couple of other annoying "mandatory" features Apple imposes on us now, that and lagging issues, the OS seems to be functioning with minor issues. This, by far, is the most annoying and unfriendly version of Mac OS X I've ever upgraded to (next to Lion). I could revert back to Snow Leopard, which was running amazing on my Mac Pro, but I won't be able to upgrade/update many of my apps which require Lion or higher. Stuck between a rock and a hard place.