comments reply script not working

Don’t link the script file directly. Enqueue it instead, e.g. in functions.php:

function mytheme_enqueue_comment_reply() {
    // on single blog post pages with comments open and threaded comments
    if ( is_singular() && comments_open() && get_option( 'thread_comments' ) ) { 
        // enqueue the javascript that performs in-link comment reply fanciness
        wp_enqueue_script( 'comment-reply' ); 
    }
}
// Hook into wp_enqueue_scripts
add_action( 'wp_enqueue_scripts', 'mytheme_enqueue_comment_reply' );

You can also do this, in the document head, prior to the wp_head() call:

<?php
// on single blog post pages with comments open and threaded comments
if ( is_singular() && comments_open() && get_option( 'thread_comments' ) ) { 
    // enqueue the javascript that performs in-link comment reply fanciness
    wp_enqueue_script( 'comment-reply' ); 
}
?>

EDIT:

Hooking into wp_head, rather than e.g. wp_print_scripts, is important. The wp_print_scripts does not work in the same way that wp_print_styles does, to output stylesheet links.

So: if you’re using wp_print_scripts, change the hook to wp_head.

EDIT 2:

Based on your pastebin-linked code, have you tried the following, to rule out potential issues?

1. Remove callback function from wp_comment_list()
2. Move wp_comment_list() call to before comment_form() call
3. Remove the argument array from comment_form()

I don’t know that any of those will solve your problem, but they may help us track down its origin.