Your device is most definitely rooted... however I believe on the nook dev site, there is a page dealing with this... From the sounds of it you are using the nooklauncher over the ru version. To set nooklauncher as default you have to push the apk packet they have on the site to your nook, overwriting the original home.apk. Then you wont need to continue to select which one you want to use. Hopefully this helps. Sorry I can't help with anything else.
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