It is really weird because it only happens on subdomains, subfolders are not affected. I am using your htaccess code and made a folder accesible by test.example.com and example.com/test. Only on test.example.com I get the weird characters. And I am using a blanco copy of CI. It seems to be a problem on CI their side as I did not modify anything else except for setting the htaccess you provided me.