I have a similar issue. Except comments appear to be working correctly on posts but I am showing all comments from the site on all pages. I too have recently upgraded to 2.9.1, I have tried shutting off plugins, changing themes (I use Arras) fixes this problem, but causes others, with the default theme it will give the correct number of comments but show none and will not provide a comment box and say that comments are disabled when they are in fact enabled.
I have not tried resetting the plugins folder yet, will try this later this afternoon when I have time.
