Sup Folks,
A simple solution that worked for me WITHOUT tweaking core WP Minify files was to enqueue all my scripts in the header instead of the footer. When you enqueue your files in your functions.php file declare FALSE at the end of the array to force scripts to load in the header.
ex.
<?php wp_register_script('modernizer', get_template_directory_uri() . '/js/modernizr.js', 'jquery', '2.6.2', FALSE ); ?>
Hope that helps.