Are you saying that your computer is not recognizing your NC, or that your NC is not charging? Does the charger work when plugged into a wall outlet? The NC does not charge with a usb. See page 12 of user guide.
It's not likely that the USB cable for the Nook is shorting out your mouse, your computer is capable of concurrently using a large number of USB devices. Are you having problems with your mouse while the Nook is connected? Are you able to connect the Nook OK? When you do connect your nook are you doing a safely eject every time you disconnect the Nook from your PC?