I have a patch for you that can work until the developper finds a solution:
Go to your file: wp-content/plugins/kimili-flash-embed/kml_flashembed.php
Under the line that reads :
$querystring = join("&", $this->parseFvars($fvars));
Just put these lines:
$movie = str_replace('”', "", $movie);
$movie = str_replace('??', "", $movie);
Because after an WP4.0 update, the plugin will add extra quotes on the path of the swf files in the <object> element, which makes a 404. And of course, not loading your file.