I don't think autonooter will affect your windows computer (it doesn't help you install any drivers on your computer). It sounds like the SD card hasn't been property created, especially if the Nook appears to boot normally. I would walk through the steps to put the autonooter image on the card again.
As a suggestion, you might try this suggestion below as an alternative. It won't root your Nook, but it should boot your nook w/ android 2.2. You should use the same steps to create the SD card as autotnooter.
https://www.mobileread.com/forums/sho...5&postcount=10
that will help you confirm you are creating the sd card properly.