Just wanted to let you guys know that I fixed the reply to comments and threaded comments so it is working properly now.
Had to upgrade to a newer version of the theme I was using and then implement the WordPress Nested comments option in the Settings-Discussion area that is available for 2.8 and higher versions of WordPress.
I wish I could have used a plugin instead since they come with more options, but none of them seem to be working with this theme, but at least the reply option is back.
WordPress Nested Comments in Versions 2.8 and Higher
The simplest way to add somment nesting, if your blog theme supports it, as not all of them do is to use the WordPress feature for nested comments by going to Settings – Discussion and selecting nest comments. Once you select it you will know if it will work with your theme. Or you can try a plugin.
Best Reply To Comments and Threaded Comments Plugins
If you are interested in getting threaded comments or the option for commenters to reply to other comments on your blog here are some good plugins for that purpose:
WordPress Thread Comments Best! - This is the best one with the most options and integrates the reply feature AND nesting of replies in a threaded fashion.
1. Admin selection of commenters getting emails when someone replies to their comment.
2. Nesting and threading of replies in a neat design.
3. Admin can reply within the admin dashboard.
4. Automatically provides the @previous commenter name in replies.
Comment Toolbar – Adds comments navigation, quote and reply buttons (with links or images) at the beginning or end of each comment. You can customize every aspect of the toolbar and it now has smooth scrolling as well. One drawback of this one is that nesting and threading of the replies is not included.
Brian’s Nested Comments – Not sure if this one is still supported, but looks interesting.