I had this same problem. I believe the device drivers that are provided for the NC from NookDevs are badly written or something. I had problems with Windows 7 on two different computers, have had to delete the drivers several times and have had problems with the device showing up (it registers as offline) almost every time I try to connect it after the initial time I get it working.
The next problem I had with this whole rooting process is my NC would freeze during shutdown sometimes. It would sometimes not boot. I played with it many times, but for now I'm going to wait for better drivers and firmware before doing anything else. I have restored my NC to factory settings and it is working perfectly for what I need it to do (read books in dark situations). I don't like the idea of making this thing an expensive paper weight.

I love it that much just the way it is.
I did however install everything I could under the rooted firmware. Dolphin HD was such a pleasure. The live wallpapers were cool. I could go on and on about all the exciting stuff I got off the market. I know I seem to be contradicting myself here, because I loved playing with all the Android stuff, but this thing is first and foremost an excellent ebook reader for me. Books load much faster from the book icon under the stock firmware too. I don't know. I might decide to go back to rooted in a month or so.