This may be one of your problems, if I remember correctly...
If you are downloading your
whole collection from the Reader Library, don't hit the "
Download all checked" button until you have checked
all the ebooks (there may be several pages of them) that you want to download.
If you are downloading
one page at a time, of your collection, remember to
uncheck the boxes on the current page before going to the next page, otherwise the current page will be re-downloaded again when you hit the "Download all checked" button on subsequent pages...and again every time you hit that "Download all checked" button.
Clear as mud.
I did this the wrong way the first time and downloaded multiple copies of every book, except of course the last page.