Thanks and aargh! You caught a bug in version 1.3.2 that was introduced by one of the changes. You can fix it for now by changing this line in qa-theme.php:
if (strpos($key, 'custom')===0)
... to ...
if ( (strpos($key, 'custom')===0) && ($key!='custom_header') && ($key!='custom_footer') )
Sorry about that - I'll try to release a fixed version asap.