Theme not calling Jquery properly

If you register a script with wp_register_script() it is not neccessary to pass all the options in wp_enqueue_script() again.

You can register the script in a central place and use the enqueueing it in diffenrent files.

functions.php
wp_register_script( 'theme_script', 'path/to/script.js', array( [dependencies] ), '1.0', true );

[...]

if ( $condition )
  require_once 'file1.php';
else
  require_once 'file2.php';

file1.php
wp_enqueue_script( 'theme_script' );

file2.php
wp_enqueue_script( 'theme_script' );

Adding a source to wp_enqueue_script() after registering it earlier will lead to some trouble. Let’s have a look into the core file ( wp-includes/functions.wp-scripts.php )

if ( $src ) {
  $_handle = explode('?', $handle);
  $wp_scripts->add( $_handle[0], $src, $deps, $ver );

What does this mean for your theme?

At first you register a script with the handle “jquery” and the source “http://ajax.googleapis.com/ajax…“. Than you enqueue a script with the handle “jquery” and the source “http://ajax.googleapis.com/ajax…“.

Look at the core code: if ( $src ) means, if there is a source passed with wp_enqueue_script(), apply the first part of the source (before the ? ) to the handle and register a script with this handle and this source.

So you registered a script with the handle “jquery” and the source “http://ajax.googleapis.com/ajax…” with wp_register_script(). And you registered and enqueued a script with the handle “http://ajax.googleapis.com/ajax…” and the source “http://ajax.googleapis.com/ajax…“. Later you try to enqueue a script (comment-reply) that depends on “jquery“, but the jquery script is only registered but not enqueued.

This leads to unexpected behavior.

Dependencies should be passed as array (array( 'jquery' )) (see Codex here and here). And in development turn WP_DEBUG on and check if the files exists. There is really no need to deregister a core script and re-registering the same file again. If you need a unminified version (e.g. for debugging), use the SCRIPT_DEBUG constant.

Your script should look like this:

function init_scripts() {
wp_deregister_script( 'jquery' );

// Register Scripts
if ( ! defined( 'SCRIPT_DEBUG' ) && ( defined( 'WP_DEBUG' ) && true == WP_DEBUG ) )
 define( 'SCRIPT_DEBUG', true );

$modernizr_file = get_bloginfo('template_url') . '/js/modernizr-1.5.min.js';
if ( defined( 'WP_DEBUG' ) && true == WP_DEBUG && ! file_exists( $modernizr_file ) )
  throw new Exception( 'File not found for JS modernizr:' . $modernizr_file );

wp_register_script( 'modernizr', $modernizr_file, '', 1.5, false );
wp_register_script( 'jquery', 'http://ajax.googleapis.com/ajax/libs/jquery/1.4/jquery.min.js', '', '1.4.2', true );

// Enqueue scripts, dependencies first
wp_enqueue_script( 'jquery' );
wp_enqueue_script( 'modernizr' );

if ( get_option( 'thread_comments' ) )
  wp_enqueue_script( 'comment-reply' );

}