Seem to have solved it, but not sure which step was the successful one.
The steps I took were:
1. Take ownership of Program Files folder for Administrators Group (with Replace owner of sub containers and objects checked). I had previously done this without success and again on it's own it did not work.
2. In Program Files folder Properties/Security/Advanced/Permissions I chose "Inherit from parent the permission entries ...explicitly defined here". Again this on its own did not solve the problem. When I checked effective permissions for the Administrators Group in this area it again showed I had full permissions.
3. In Program Files folder Properties/Sharing/Permissions there was only "EVERYONE" listed. I added the Administrators Group to this and gave it full access. This seemed to work.
4. I then repeated these all steps with the My Document/'logged in user' folder and checked on each step. This did not work until I repeated step one after steps 2 and 3.
Thank goodness the problem is solved but I don't understand entirely whats going on.
Thanks for your help guys.