The page here: http://www.jetbrains.net/confluence/display/TCD3/Authentication+Settings
could have a mention along the lines of the following.
Before configuring TeamCity to use AD Authentication, login as your admin user and set the default role for new users to System Administrator.
Configure Team City to use AD authentication.
Login to TeamCity with your windows username and password. You should now have system administration access.
Reconfigure the default role assigned to new users to one more appropriate.
I successfully logged in after configuring TC for AD with a projectviewer only role. Switching it back to DefaultLoginModule brings back the users from that, not the new AD users registered for the NTDomainLoginModule, so I was unable to fix my login with the previously configured admin user, which no longer worked in AD mode. Just a little gotcha.