The correct way to load html5shiv in Genesis Theme Framework. See relative WPSE answer regarding this - http://wordpress.stackexchange.com/a/214460/43806. Currently the `load-scripts.php` file looks a little confused. It registers the html5 script, but then decides to add it using `wp_head`. It's also calling the $wp_scripts global which isn't n…

load-scripts.php

<?php
/**
 * Genesis Framework.
 *
 * WARNING: This file is part of the core Genesis Framework. DO NOT edit this file under any circumstances.
 * Please do all modifications in the form of a child theme.
 *
 * @package Genesis\Assets
 * @author  StudioPress
 * @license GPL-2.0+
 * @link    http://my.studiopress.com/themes/genesis/
 */

add_action( 'wp_enqueue_scripts', 'genesis_register_scripts' );
/**
 * Register the scripts that Genesis will use.
 *
 * @since 2.0.0
 *
 * @uses GENESIS_JS_URL
 * @uses PARENT_THEME_VERSION
 */
function genesis_register_scripts() {

	$suffix = defined( 'SCRIPT_DEBUG' ) && SCRIPT_DEBUG ? '' : '.min';

	wp_register_script( 'superfish', GENESIS_JS_URL . "/menu/superfish$suffix.js", array( 'jquery', 'hoverIntent', ), '1.7.5', true );
	wp_register_script( 'superfish-args', apply_filters( 'genesis_superfish_args_url', GENESIS_JS_URL . "/menu/superfish.args$suffix.js" ), array( 'superfish' ), PARENT_THEME_VERSION, true );
	wp_register_script( 'superfish-compat', GENESIS_JS_URL . "/menu/superfish.compat$suffix.js", array( 'jquery' ), PARENT_THEME_VERSION, true );
	wp_register_script( 'skip-links',  GENESIS_JS_URL . "/skip-links.js" );
	wp_register_script( 'drop-down-menu',  GENESIS_JS_URL . "/drop-down-menu.js", array( 'jquery' ), PARENT_THEME_VERSION, true );
	wp_register_script( 'html5shiv', GENESIS_JS_URL . "/html5shiv$suffix.js", array(), '3.7.3' );

}

add_action( 'wp_enqueue_scripts', 'genesis_load_scripts' );
/**
 * Enqueue the scripts used on the front-end of the site.
 *
 * Includes comment-reply, superfish and the superfish arguments.
 *
 * Applies the `genesis_superfish_enabled`, and `genesis_superfish_args_uri`. filter.
 *
 * @since 0.2.0
 *
 * @uses genesis_html5()      Check for HTML5 support.
 * @uses genesis_get_option() Get theme setting value.
 */
function genesis_load_scripts() {

	//* If a single post or page, threaded comments are enabled, and comments are open
	if ( is_singular() && get_option( 'thread_comments' ) && comments_open() )
		wp_enqueue_script( 'comment-reply' );

	//* If superfish is enabled
	if ( genesis_superfish_enabled() ) {

		wp_enqueue_script( 'superfish' );
		wp_enqueue_script( 'superfish-args' );

		//* Load compatibility script if not running HTML5
		if ( ! genesis_html5() )
			wp_enqueue_script( 'superfish-compat' );

	}

	//* If accessibility support enabled
	if ( genesis_a11y( 'skip-links' ) ) {
		wp_enqueue_script( 'skip-links' );
	}
	
	if ( genesis_html5() ) {
		wp_enqueue_script( 'html5shiv' );
		wp_script_add_data( 'html5shiv', 'conditional', 'lt IE 9' );
	}
	
}

add_action( 'admin_enqueue_scripts', 'genesis_load_admin_scripts' );
/**
 * Conditionally enqueue the scripts used in the admin.
 *
 * Includes Thickbox, theme preview and a Genesis script (actually enqueued in genesis_load_admin_js()).
 *
 * @since 0.2.3
 *
 * @uses genesis_load_admin_js() Enqueues the custom script and localizations used in the admin.
 * @uses genesis_is_menu_page()  Check that we're targeting a specific Genesis admin page.
 * @uses genesis_update_check()  Ping http://api.genesistheme.com/ asking if a new version of this theme is available.
 * @uses genesis_seo_disabled()  Detect whether or not Genesis SEO has been disabled.
 *
 * @param string $hook_suffix Admin page identifier.
 */
function genesis_load_admin_scripts( $hook_suffix ) {

	//* Only add thickbox/preview if there is an update to Genesis available
	if ( genesis_update_check() ) {
		add_thickbox();
		wp_enqueue_script( 'theme-preview' );
		genesis_load_admin_js();
	}

	//* If we're on a Genesis admin screen
	if ( genesis_is_menu_page( 'genesis' ) || genesis_is_menu_page( 'seo-settings' ) || genesis_is_menu_page( 'design-settings' ) )
		genesis_load_admin_js();

	//* If we're viewing an edit post page, make sure we need Genesis SEO JS
	if ( in_array( $hook_suffix, array( 'post-new.php', 'post.php' ) ) ) {
		if ( ! genesis_seo_disabled() && post_type_supports( get_post_type(), 'genesis-seo' ) ) {
			genesis_load_admin_js();
		}
	}

}

/**
 * Enqueues the custom script used in the admin, and localizes several strings or values used in the scripts.
 *
 * Applies the `genesis_toggles` filter to toggleable admin settings, so plugin developers can add their own without
 * having to recreate the whole setup.
 *
 * @since 1.8.0
 *
 * @uses GENESIS_JS_URL
 * @uses PARENT_THEME_VERSION
 */
function genesis_load_admin_js() {

	$suffix = defined( 'SCRIPT_DEBUG' ) && SCRIPT_DEBUG ? '' : '.min';
	wp_enqueue_script( 'genesis_admin_js', GENESIS_JS_URL . "/admin$suffix.js", array( 'jquery' ), PARENT_THEME_VERSION, true );

	$strings = array(
		'categoryChecklistToggle' => __( 'Select / Deselect All', 'genesis' ),
		'saveAlert'               => __( 'The changes you made will be lost if you navigate away from this page.', 'genesis' ),
		'confirmUpgrade'          => __( 'Updating Genesis will overwrite the current installed version of Genesis. Are you sure you want to update?. "Cancel" to stop, "OK" to update.', 'genesis' ),
		'confirmReset'            => __( 'Are you sure you want to reset?', 'genesis' ),
	);

	wp_localize_script( 'genesis_admin_js', 'genesisL10n', $strings );

	$toggles = array(
		// Checkboxes - when checked, show extra settings
		'update'                    => array( '#genesis-settings\\[update\\]', '#genesis_update_notification_setting', '_checked' ),
		'content_archive_thumbnail' => array( '#genesis-settings\\[content_archive_thumbnail\\]', '#genesis_image_extras', '_checked' ),
		// Checkboxed - when unchecked, show extra settings
		'semantic_headings'         => array( '#genesis-seo-settings\\[semantic_headings\\]', '#genesis_seo_h1_wrap', '_unchecked' ),
		// Select toggles
		'nav_extras'                => array( '#genesis-settings\\[nav_extras\\]', '#genesis_nav_extras_twitter', 'twitter' ),
		'content_archive'           => array( '#genesis-settings\\[content_archive\\]', '#genesis_content_limit_setting', 'full' ),
	);

	wp_localize_script( 'genesis_admin_js', 'genesis_toggles', apply_filters( 'genesis_toggles', $toggles ) );

}

If you aren't able to get rid / deprecate genesis_html5_ie_fix() for some reason and the above example doesn't work, just make sure it's hooked into wp_enqueue_scripts.

add_action( 'wp_enqueue_scripts', 'genesis_html5_ie_fix' );
/**
 * Load the html5 shiv for IE8 and below.
 *
 * @since 2.0.0
 *
 * @uses genesis_html5() Check for HTML5 support.
 *
 * @return Return early if HTML5 not supported.
 *
 */
function genesis_html5_ie_fix() {

    if ( ! genesis_html5() )
        return;

    wp_enqueue_script( 'html5shiv' );
    wp_script_add_data( 'html5shiv', 'conditional', 'lt IE 9' );

}

Also we shouldn't have to access the $wp_scripts global.

For users that stumble across this that wants to use this update without editing Genesis you can easily do so in your child functions.php like this...

/**
 * Load HTML5shiv and Respond Correctly (requires html5 theme support)
 * 
 * @link https://github.com/salcode/bootstrap-genesis/issues/128
 */
if ( genesis_html5() ) {
    remove_action( 'wp_head', 'genesis_html5_ie_fix' );
    add_action( 'wp_enqueue_scripts', 'bsg_html5_shiv_respond_js_add_last' );
}
function bsg_html5_shiv_respond_js_add_last() { 
    wp_enqueue_script( 'html5shiv' );
    wp_script_add_data( 'html5shiv', 'conditional', 'lt IE 9' );
}

You can also leverage a cdn by and adding this instead.

     wp_enqueue_script( 'html5shiv',
        'https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js',
        array(),
        false,
        false
    );