Hey, thanks for the heads-up. I've noticed that a few times. It's not a CSS bug -- it's a programming issue on LJ's part. (CSS is actually pretty limited and mostly affects appearance and not actions; for example, I can't get dates to display on collapsed threads because they're programmed not to display).

LJ's most recent release post (http://lj-releases.livejournal.com/72149.html) says there's a ticket about losing comment position, though it might only have been filed for the S1 style. When I'm more awake, I'll see about filing a ticket for customized S2 pages.