For me, the upgrade went painlessly until I completely embraced the themes. I split my Index page into Header, Footer Sidebar etc. Then my comments stopped working - nothing shows up. I tried replacing the comments.php file with the default, but it made no difference. My comments.php file worked fine before, and it still works fine on my single.php page.
Is it something to do with calling it mulitiple times on the page? I don't like using the popup. I use ScriptyGoddess' show/hide comments, which works fine. _Worked_ fine. I've tried the other suggestions in this thread (those I understood). Anybody?