Article threading isn't working the same now as in old-Pan.  Since they say "a picture is worth a thousand words," I'll display the problem with screenshots.

Here's a snap of old Pan with "Show Matching Articles/Match Unread Articles":

http://doug.freeshell.org/files/pan1.png

And the same "Show Matching Articles/Match Unread Articles" in new Pan.

http://doug.freeshell.org/files/pan.png

It's exactly the same, which is fine.  However, article threading is very untidy this way, which is why I don't use that view very much.  The fix, however, is to use "Show Matching Articles' Threads/Match Unread Articles".  Now the header display looks much cleaner in old Pan:

http://doug.freeshell.org/files/pan3.png

However, in new Pan, selecting "Show Matching Articles/Match Unread Articles" in the menu doesn't change the header Pane threads at all.  The screenshot would be exactly the same as "pan.png" above.

If it's not an outright bug, I think old Pan's "Show matching articles' Threads" feature was much nicer.