I have a Nook HD+/HDplus which shipped with BN 2.0.3 Stock ROM, and that does not have any of these issues. It is an earlier build though.
Perhaps this fault occurs with early devices, and those which are being manufactured now? I'd simply go for a warranty. I know it's a hassle, but it's better to do it now, whilst you still have the warranty option available. You never know, it could get worse and eventually affect the whole screen. To mix matters up more, this could occur when you're outside your warranty.
I'd do a backup of your current setup, whichever way you prefer, be it CWM backup/TitaniumBackup (as long as you get everything backed up); then get a warranty replacement. After that, you should have no worries; and can be comfortable that there will be no further hardware issues with the screen.
All the best guys/girls!
