To make compatibility WPGlobus and Popups – WordPress Popup plugin you can use next piece of code

add_filter( 'spu/popup/content', 'wpglobus_popups_compatibility', 10, 2 );
function wpglobus_popups_compatibility( $content, $box ) {
  if ( class_exists('WPGlobus') ) {
    $content = WPGlobus_Core::text_filter( $content, WPGlobus::Config()->language );
  }
  return $content;
}

just place it in functions.php file of your theme

UPDATE from 13.01.2016:
WPGlobus support was added in plugin Popups – WordPress Popup version 1.4.4