I just upgraded from 2.2 to 2.7. Everything is went perfectly smoothly except for the comment_popup_link function... I thought it was my theme, but it doesn't even work in the default or classic themes. When you click on the popup comment link, instead of it pulling up whatever you have coded into the comments-popup.php file, instead it pulls up the permalink for that post. It doesn't access comments-popup.php at all... completely bypasses it.
Here's the blog: http://www.mclellanblog.com
Any ideas as to how to fix this? Or do I need to downgrade WP? Without the popup comments working, no one can leave comments on our blog at all due to how the entire thing is constructed.