Thanks for the suggestions Grim, I tried doing as you say with the run as admin, and also not opening a project and just adding the paths to search, then closing but on restart cubase still does not show any paths. I also tried with the user access control set to never but that did not help either. Also the user profile I am using is an administrator.
So thinking you were on to something with the permissions idea, I created a new user with admin rights and logged on as the new admin user and it works without any issues.
Thanks again for your help Grim