I reported this like the 2nd day after I got my Kindle 2. It's a well-documented but little-known problem. If you got over a day or so with wireless off, Kindle stops timestamping the books correctly when up access them, causing them to go to the end of the list. Only way to fix it is turn wireless back on, then re-access those books.
https://www.mobileread.com/forums/showthread.php?t=40337