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same problem - no solution
I got my Nook last December and softrooted immediately. Got same problem as you. Some of the tags appear, others simply do not. I spent hours carefully tagging my 70+ "test" books in Calibre -- but despite all my efforts I still get some tags appearing to sort and others seem lost.
In addition, I too experienced a sudden rush of new tags - most of which I never used or instigated. I asked for help on this forum, but it didn't seem as if anyone else was experiencing problem.
I finally gave up. I don't use the tags at all b/c they are so inconsistent.
Sorry .... wish I could help.
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