Some Programs Ignore Key / Mouse Events?

I use AutoHotKeys to remap my windows key, and use Logitech Setpoint to map the middle mouse button to close the currently focused program. This worked fine in Windows 7.

Now with Windows 10, it works "most" of the time. For all program like Firefox and File Explorer and whatnot its fine - when I click the middle mouse button the window closes, and when I click the windows key it does the remap I want. But for other focused programs, like notepad.exe, regedit and compmgmt.msc snapin these events don't work now. The middle mouse click won't close the window and the windows key just acts normal with the AutoHotKey mapping ignored.

Its like all Windows 10 program have been recompiled for the Windows 10 release obviously, but specifically these Win10 programs seem to be one step above the internal windows message queue maybe any ignoring these message or not seeing them?