Auto Scroll Enablement during comparison
Enable auto scroll functionality in the notepad++. this will help is comparing two huge files.
Not quiet clear to which auto scroll functionality you refer to as there is a synchronized scroll functionality in npp and there is a plugin called compare which addresses this as well. Which one doesn’t do what you want? Btw. post your debug-info, which can be found under the ? menu (last menu item) if you need additional help.