Are you experiencing this when you're deleting files from collections? I ask because deleting a file out of a collection list only deletes the list entry
in the collection itself, rather than the actual book from the Reader's memory (this confused me terribly until I realized it was so).
If you're deleting the book from the main Reader entry, or from the "Books" list on the Reader (I don't mean the one under the Library entry), and the book is still
staying on the Reader, then I'd think that there's definitely something wrong, and you probably ought to talk to the customer support folks.