Strange. IF your 3.5.x was working fine it too had a Slash arguments (on by default me thinks) ... known to apache as 'acceptpathinfo' ... setting. Upgrade to 3.6.x and themes go wonky. In apache config, can be set via server config, virtual host, directory, or .htaccess and default is on.
So the upgrade of moodle lost settings upon upgrade?
Anyhoo ... all is well that ends well, I guess.
Congrats on solving your own issue!
'SoS', Ken