AHA!! That did it djpushplay, also solved my issue of having it show only how many comments were on that certain page of paged comments. Thanks a bunch for your help!
As for you hermanong, try deactivating all of the other plugins and leave threaded comments alone to see if it will work then, just my new-bie suggestion; if it works then one of the plugins are causing the issue. As for the e-mail part, I dont completely understand. Do you mean the the e-mail will send to the admin if there is a response/reply to a comment but not to the other people? Not at a 100% of what you mean by that.
Lastly, yes you can update your theme, but if the theme author did not update it, you would need to update it your self. You can always ask them to update it, but it depends on if they are willing/able. I got a premium theme and the author has disappeared, man am I pissed, but live and learn.