I had a similar issue when I upgraded from 5.1 to 5.5. I found the upgrade process had removed all the assigned rights for my domain accounts. you will have to log in to the web client using the admin@system-domain user using the password you set when installing Single Sign On, then you can set the permissions back to what you had. I hope your permissions weren't too complex.
BTW, my upgrade also removed all my distributed switches from my non-clustered hosts.