Last week, I had to perform some restore activities for a site collection that became corrupt. When I was done, users reported that permissions were gone. After logging on I found out that I wasn't able to open the Site Settings. The Site Actions > Site Settings menu option was gone?!?!?!?
After some troubleshooting I found out that during earlier steps, the site collection accidentally was set to Read-Only lock. That is why I wasn't shown any admin screens. When the lock was lifted, all started working again!