Admin user can't administer the site
If you can't do all that with the superuser (typically admin, user ID 1), checking permissions won't help, since that account has a "pass all permissions" check on nodes, modules, users, etc.

To figure this out, you can try a few things:


Go into the database and check if your admin user really has uid 1 (in the users table)
Check modules (custom modules, specifically) to see if any of them deny access to any admin pages