There are several threads on this issue. Put Stuck at 99% into the search box and have a read.
It seemed to be linked to having multiple accounts on the device, and switching between them. I know that Alex the moderator said that this issue was resolved with the latest software upgrade. If your device says it is running software version 2.1.1 and you are still having the issue, I would message Alex.
Other than that, it's a factory reset and I would only set up one account on the device until this issue is fully resolved.
'Completley power off the NOOK then press the "n" (home button) during power on. This should get it unstuck. If it doesn't work, drain the battery and once completely drained, charge your device and power on. The battery should drain quicker than usual due to the 99% screen being active.'
per RickyX an administrator.