I've encounter a couple of problems when I work with a file that's opened in two separate windows.
First if I select and copy text in one window and past it into the second window, when I return to the first window the selection doesn't disappear when I click somewhere else on the page. I need to cursor over the selection to force a redraw to remove the selection appearance.
Second when I perform any sort of editing on one window and Command+` to the second window (and before using the mouse to click on the second window's edit area) the insertion point is moved to the top of the page so that any subsequent keyboard activity results in the page redrawing at the top of page. I then have to relocate the line that I was originally at.
This makes any sort of editing between two views of the same file using a keyboard a pretty frustration experience.
I'm not going to mention a request for a split window as I think that one's been requested enough in the past. ;-)
Thanks, Ed