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It's usually a good recommendation to do this format, in the NC, immediately after the first successful bootup into the rooted system. You'll know the root was successful upon it's first boot, when you see the nook color devs android icon in the lower right corner of the animated "Nook Color" boot screen.
I've found that if I fail to do this immediately after the first bootup, that I inevitably forget to remove the card from the NC, and upon any successive bootups, the NC will attempt to root yet again from the micro-SD card rooting data. If you're like me on my first root, you thought something was wrong on the second bootup, and pulled out the micro-SD card when the screen was black, right in the middle of a re-root, which yields bad things.
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