I'm running 1.3.0.2. all is well except the menus and pages I want to disable still appear. If the user clicks on a particular item which I have "unchecked", they get the denied access page. However the links are still there.
I checked the db and the admin headings are correct in the sense that user id 2 does not have all the headings listed. But when user id 2 logs in, page loads, everything shows up.

I have another installation of the same version for another client and it seems to work flawlessly.

Any suggestions ?