I wish I could just take a screen shot but my laptop is in my locker (I am deployed)
Let me try to explain. On my Mac I created a directory called eBooks (creative eh) and that is where Calibre is storing the ebooks. Some books are under:eBook/author/book name/ebook file. Simple enough... just how I like it. Others are simply under eBook/file name.
I could be doing something wrong as I found out when changing book authors to the correct one. I am almost willing to bet that they are actually sorted correctly but maybe calibre now treats it as a different book and copies it to the right folder leaving the older one behind?