Yipee I have solved it. Somehow there was some modules in the module folder with mod_yoo_ and then a mod name, even though these files had the correct permissions they caused restricted access in modules and payments in the back office. One thing is for sure working through the issues made me appreciate prestashop and its modular system, after working with cubecart, zen, magento and of course oscommerce this was a breeze to work through. :-)