Subtheme media query CSS in Omega Kickstart subtheme
I had similar issues like this. I ended up simply overriding the CSS file in my template.php. I created a helper for me to do this. Simply run hook_css_alter and replace the file you are targeting with your own. In this case, the omega theme's grid file is here:

sites/all/themes/contrib/omega/alpha/css/grid/alpha_default/wide/alpha-default-wide-24.css


And I am replacing it with:

sites/mysite.com/themes/my_theme/css/grid/alpha_default/wide/alpha-default-wide-24.css


This is the code in my template.php

/**
 * Implements hook_css_alter().
 */
function my_theme_css_alter(&amp;$css) {
  $themePath = drupal_get_path('theme', 'my_theme');
  $newCSS = array(
    'sites/all/themes/contrib/omega/alpha/css/grid/alpha_default/wide/alpha-default-wide-24.css' =&gt; $themePath.'/css/grid/alpha_default/wide/alpha-default-wide-24.css'
  }
  _my_theme_replace_file($css, $newCSS);
}
/**
 * Helper function to replace an existing file with a new path
 */
function _my_theme_replace_file(&amp;$files, $newFile) {
  foreach($newFile as $oldpath =&gt; $newPath) {
    if(isset($files[$oldpath])) {
      $files[$newPath] = $files[$oldpath];
      $files[$newPath]['data'] = $newPath;  
      unset($files[$oldpath]);
    }
  }
}


The helper function _my_theme_replace_file simply loops through the array, finds the old path and replaces it with the new one.

I hope this helps.