Ever notice that certain comments end up out of order. I’ve encountered this issue on one of my posts and I think I discovered the cause. The problem is that I have been responding to certain comments through the admin panel and not directly on the single post page. Some of these comments are already threaded under other comments but there is no way to tell in the admin panel. It was all my fault, though and not WordPress’.

I had to go into the database and just remove the comment_parent value from my comments that were causing the problem and everything went back into place. Not an easy solution but a solution none the less. Hope that helps.