Not long ago, I discovered how to fix a minor but annoying problem on my Kindle, and I thought I'd share it here for whatever it is worth. I have the Kindle Keyboard, and I don't know if this will work with any other model.
I don't often use the wireless function, instead normally loading my books from my computer through the USB port. From time to time, my Kindle will stop sorting my Collections, and books within Collections, in my preferred order, by last date/time read. The fix seems to be to turn on wireless, and then go Home/Menu/Sync & Check for Items. The Kindle churns away for a few seconds, and once the sync is complete you can turn off wireless again.