Really don't know about Aldiko, don't use it, but in FBReaderJ you can change settings for folder where it will look up for books and I did it and now it takes books from internal storage folder Books (I created it when device was USB connected to PC).
Just wondering did you update firmware? Because I received mine a week ago from Amazon and it contained old one, but I thought that it should already had a new one
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Dmitry.