Sorry for the bit of misreading I did. I think the fact it told me that it was sending the metadata when I switched to automatic management threw me off. Or I need to sleep more. Or both.
That being said, I tried resending my books, as suggested. Specifically, I picked two and tried those, rather than the whole bunch. I've done it three times and I still don't have my covers on either one. Thoughts?
Also, as a side question, my books, when sorted by author, are on my Reader in order of first names, even though I have the author sorts set as last name, first name in Calibre. Is that another thing you have to check somewhere, or is my Reader unhappy with its new owner and out to torment me? It does look a little shady over there...