OK. This happened to me too. I have Kindle app v3.1.1. When I try to open an ebook I side loaded, I get an error message to remove the book and redownload it. I loaded the book into the Kindle\Library\ebooks folder.
I haven't tried to side load a book for a while. I have been just sending the book to my kindle/kindle app via email. Just tried now to test after reading your post. Seems I remember this happening before and then it got fixed.