Sounds like perhaps one of the books you sideloaded is corrupt. This causes all kind of weird problems because the Nook cannot index the books correctly.
Can you open all of the sideloaded books correctly on your PC using ADE? Perhaps that way you can find out which book is corrupt.
Otherwise I think the best solution is to delete all sideloaded books end search for new content so the Nook can index correctly and your My Documents view is empty.
Than put the books back one by one, or in batches, to find out which book causes the problem.
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