That really sounds like an window manager thing, not a godot issue.

I had similar issues with other programs. In my case it was PersistentWindows, which I use to make sure that the windows I open keep their position even when I disconnect my second monitor.

Or is it like in debug when stepping over scrolls the code so the cursor is always in the middle of the screen? I find that distracting and would prefer the cursor to start at the top and move down until the screen needed scrolling. Not sure if there's a setting to do that?