The ShortCut VUr addon is actually really cool. It captures your mouse and keys in blender.
Is there a way to make it start when blender opens and have it already running when loading the startup file or any file on load?
Should be possible, but you'd probably need to dive into the code.
I've naively tried and changed the default in this line:
wm.SCV_started = bpy.props.BoolProperty(default=False)
(in __init__.py ) to True.
Which did get the addon running on start-up, but it didn't show any key presses, I had to stop it and then start it again to actually show something...Must be something else you also need to change...
But the best thing might be to ask Jayanam himself.