Sorry, I haven't updated my profile info for a while. I'm actually using a Kindle Fire now. I always sort my book my title, because again, I'm anal like that.

I did check for strange metadata in Calibre, but I didn't notice anything different that would cause it to sort weird. And before the issue actually started appearing, I hadn't connected my Kindle to Calibre since November, when it released. So it acted fine for almost 6 months before it started sorting them oddly.
As for the second question, I ended up finding them in the Documents section of the Fire, which is strange, since it's the same format as every other book that shows up normally under Books. No idea why.
Thanks for your response.