If you have 3 levels of folders (Genre, Author, Series), are the books duplicated in each one? I am wondering if the LC has trouble with multiple copies of the same book when it re-indexes the library with the data from the SD Card.
The only thing I can think is to try authorizing the LC and see if it makes a difference. You never have to use the LC with ADE again, after you do, and it doesn't make sense that it will make a diff, but who knows?
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