So apparently "JetPack Comments" broke my comments, causing recent comments to get posted to the wrong thread. They claim it's not their fault, saying that it's due to a lack of implementation of the comment_form() function in WordPress, but Atahualpa seems to support this just fine. Well, anyhow, for now I'll be disabling JetPack Comments on my blog. So if you want to comment, you'll have to sign up. I know. It's a pain. I'll get it fixed.
Update 6/10/2015: After switching themes to TwentyFifteen, the problem seems to be gone. JetPack Comments re-enabled.