When you try to reroot, have you set it back to facotry.. then register it with B&N and then autonooter?
I've so far ran autonooter against three different NC's, and haven't had an issue... Also, have you tried to remake the SD card image?? (i.e. repeat the step to create the autonooter card). If I get time at work today, I'll try and see if I can pull the nookcolor tools off of mine.. but I seriously recommend trying to redo the card, then do the reset of your device (using the boot 8x failure feature, then wipe/deregister).. once it's back up.. reregister (if you want to use it as an ereader). Then try autonooter.. also use the autonooter that goes with whatever version of Nook it's ruhning (I recommend upgrading to the 1.0.1 version, as autonooter is much easier that way).
Good Luck.!