I imagine it could have something to do with the physical fixedness of a book. I can remember the positions of the line breaks in some of my favourite books as a child and it wouldn't surprise me if the physical layout of the words on the page (and how far through the book you are) somehow factored into the way the brain stores the memories of reading the book.

With an ebook you have the same little device with exactly the same dimensions for every book (no memorable covers or different formats) and there's no physical indication of how far through the book you are. And you can change the font size.