Am not sure if this is related, but I remember reading in some threads about the original Nook (not the NC) that some people were reaching a limit in terms of how many books the Nook would handle at once. I think around 1200-1400 people were experiencing problems, but I think the symptom was that the library software would just totally crash. Not identical to what you are seeing, but I wonder if you are hitting a same type of wall in what the NC software will handle at once. I sure hope not, being a large collector myself, but I can't find any other posts on the subject aside from one on the BN boards where a dev mentioned they tested a "locker" (??) of 2500 mixed media files.
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