this happened to me yesterday. I do not like auto check and I know that I unchecked the option because I like to look for better seats as others get upgraded. When I went to do that, I was annoyed to find that I'd already been auto checked in.

I haven't found that it affects my place in the upgrade queue. if I check in at t-24, I start at on top and wind up 10 or less when the flight boards. I once checked in t-1 and jumped to the top of the list for 1 open seat and got it.