3.4.1 update issue. Most admin functionality lost

I upgraded to the latest version of WP 3.4.1 yesterday and all was fine as I worked in there for hours. However when I logged into my site today I had lost much of the functionality in the admin.

In the admin there are no options under the Appearance or Settings menus other than the options for one of my plugins. I am unable to manage plugins as that option is not in the admin menu. The only real admin tasks I can perform is the management of users.

So far I have manually disabled all plugins by renaming the plugins folder. I have also followed all steps to perform a manual install. Neither step made any difference.

If I manually navigate to a missing admin page by typing in the url directly I get the following: You do not have sufficient permissions to access this page.

Thank you for any help in resolving this