Create Create New Module Position

You forgot to add necessary changes to display new module correctly in: 

http://www.yootheme.com/themes/documentation/customizing/create-a-new-module-position

templates/yoo_yourtemplate/js/template.js
make changes everywhere you find the module position you copy and paste to a new one. And not only in the one displayed in documentation

templates/yoo_yourtemplate/config
also add changes to your new position in this file - copy the one you need, paste and rename it. It does not say anything about this file in documentation