Post Content Displaying Below ALL Shortcodes Content

Are your shortcodes setup correctly? This usually means that your shortcode handling is echoing the shortcode content instead of returning it as a string.

For your case, while you are including a file in your shortcode, I doubt that you have the file setup to return the output instead of echo’ing it.

Try this instead:

function free_ms_cms( $atts, $content = null ) {
   $free_ms = TEMPLATEPATH . '/get-free-ms.php';
   ob_start(); //start an output buffer to capture any output
   include($free_ms);
   return ob_get_clean(); //return the current buffer and clear it
}
add_shortcode( 'free-ms', 'free_ms_cms' );