Interesting, it sounds like either the .apk that does the rooting isn't getting installed or whatever causes that .apk to run when you go to home isn't working. Since that was one of the few parts of the root procedure I didn't fully dissect/understand I'm not sure what exactly could be causing the problem.
I'd suggest going to the nookdevs IRC channel and asking in there. I got some good help tracking down my issue with registration getting lost (still haven't solved the problem, but the questions I asked were answered quickly to help me investigate.)
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