Reload Startup File Causes Blender to Stop Responding Whenever I use Ctrl+N to reload my startup file, Blender stops responding for about a minute. If I use File> Reload Startup File it works instantly. I personally prefer using the shortcut, so this is rather annoying.

Is there a specific reason that Ctrl+N would take longer?

Windows 10, Blender 2.77a
use "file" -> "load factory settings", followed by "file" -> "save startup file".  

the reason it's slow because you may have changed your startup file to a custom blend file that uses alot of memory.