There's some good speculation that it could be for hardware reasons. Lots of reports of Nooks with misaligned / problematic microUSB ports, plus the reports we've all heard of touchscreens with issues, etc.
I doubt it is to make the device less rootable. That's something they would chase later with a firmware update, not by spending a bunch of money to pull units.
I'd guess 2.2 or hardware/software issues of some sort.
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