Another change is that comments with scores of -4 are collapsed, regardless of how the preferences are set. Preferences can still be used to collapse more comments.
I normally use LW without JS, so it's a big hassle for me to uncollapse comments. This also means that I don't see recent comments in the sidebar, which means that I didn't realize that everyone was seeing them (as opposed to the few people who go to the recent comments page) and was confused by all this concern about them. I don't have much experience with them, but they seem of dubious value to me. A simpler solution would have been just to delete them.
I just found out that a new website feature was implemented 2 days ago. If a comment is voted to -4 or below, it and all replies and downstream comments from it will be hidden from Recent Comments, and further replies in that subthread will incur 5 karma points penalty. The hiding, but not karma penalty, applies retroactively to comments in that subthread posted before the -4 vote.
This seems to be worth a discussion post since most people are probably still voting things to below -3 without knowing the new consequences of doing so.