I have logging enabled and over the past two days the computer has shutdown successfully or remained running. I am trying to replicate the conditions that generate the behaviour.
It did not shutdown last night. This morning I reset the auto-shutdown time to several minutes in the future. I put the computer to Sleep. After about 15 minutes, I checked and it was still running. I don't see anything obvious in the Console log, filtered for 'tunnelblick'. On the second run this morning, I preceded it with a VPN connection and disconnection:
17/09/2017 22:55:00.403 Tunnelblick[1897]: DB-SD: Initiated computer shutdown
17/09/2017 23:05:00.848 Tunnelblick[1897]: DB-SD: logoutContinuedHandler: Confirmed logout, or computer shutdown or restart.
17/09/2017 23:05:00.848 Tunnelblick[1897]: DB-SD: TunnelblickShutdownUIHandler: invoked
17/09/2017 23:05:01.230 Tunnelblick[1897]: DB-SD: willLogoutOrShutdownHandler: Received 'NSWorkspaceWillPowerOffNotification' notification
17/09/2017 23:05:01.230 Tunnelblick[1897]: setShutdownVariables: invoked, but have already set them
17/09/2017 23:05:01.230 Tunnelblick[1897]: applicationShouldTerminate: termination because of shutdown; delayed until 'shutdownTunnelblick' finishes
17/09/2017 23:05:01.230 Tunnelblick[1897]: DB-SD: shutDownTunnelblick: started.
17/09/2017 23:05:01.230 Tunnelblick[1897]: DB-SD: shutDownTunnelblick: Starting cleanup.
17/09/2017 23:05:01.231 Tunnelblick[1897]: DB-SD: cleanup: Entering cleanup
17/09/2017 23:05:01.231 Tunnelblick[1897]: DB-SD: cleanup: Skipping cleanup because computer is shutting down or restarting
17/09/2017 23:05:01.231 Tunnelblick[1897]: DB-SD: shutDownTunnelblick: Cleanup finished.
17/09/2017 23:05:01.231 Tunnelblick[1897]: Finished shutting down Tunnelblick; allowing termination
18/09/2017 06:29:42.767 Tunnelblick[2796]: Tunnelblick: OS X 10.11.6; Tunnelblick 3.7.2 (build 4850)
18/09/2017 06:30:02.128 Tunnelblick[2796]: Bartender: Loaded BartenderHelperTwoOneThree
18/09/2017 06:30:02.529 Tunnelblick[2796]: Sparkle: ===== Tunnelblick =====
18/09/2017 06:30:02.530 Tunnelblick[2796]: Sparkle: Verified appcast signature
18/09/2017 07:35:55.170 Tunnelblick[2796]: Keychain item retrieved successfully for service = 'Tunnelblick-Auth-Australia - Sydney' account = 'username'
18/09/2017 07:35:55.183 Tunnelblick[2796]: Keychain item retrieved successfully for service = 'Tunnelblick-Auth-Australia - Sydney' account = 'password'
P.S. I will logout of my regular account and try a scheduled shutdown in my clean admin account.