So today I needed to investigate certain settings of a site collection in our dev environment. I went to the web site but cannot see Site Settings in the Site Actions menu at all. I checked Central Admin and I am a Farm Administrator, as well as Site Collection Administrator for that site collection. When I used SharePoint Mananger (SPM) to update a property of a list I get an Unauthorised Exception. I knew this was not normal because I know I should be able to update this property through SPM.
It turns out the site collection was locked.
Use this command to check if the site is lock:
stsadm -o getsitelock -url http://server/siteCollection
If the site is lock, use this command to unlock it:
stsadm -o setsitelock -url http://server/siteCollection -lock none
Site Settings came back, and everything else was the way they should be after I unlocked the site collection.