It looks like this is the critical output from that ticket:
"The redirect that it turned off is the .htaccess redirect. Your sites are loading the secure page because the home and siteurl values are set to the secure URLs, not because of a .htaccess redirect."
This indicates that the redirection isn't happening due to anything that is setup in the .htaccess, but in the WordPress database itself, which isn't how the WordPress Toolkit handles the change. Does that help clear things up? For more details, it would be best to reply to the direct directly as we have access to the server there.