I get regulary warnings in the watchdog like "user/sites/all/themes/xxx/js/respond.min.js", where user can be different directories.
I think there is an error in line 78 in html.tpl.php:
<script src="<?php print path_to_theme();?>/js/respond.min.js"></script>
It should read:
<script src="<strong>/</strong><?php print path_to_theme();?>/js/respond.min.js"></script>
(a / at the front).