Since I updated Tuesday's upgrade I noticed when I shut down the computer screen goes black but the system does not shut down all the lights stay on. I have to shut down by the power button.
Try and perform a system restore to a time prior to the update. See if that brings back your system's shut down functionality. In your current state, perhaps see if any device is being flagged with a yellow exclamation mark in Device Manager.
This could simply be a process that fails to shutdown properly, thus holding the Windows shutdown up. Next time when you're ready to shutdown open an elevated command prompt and enter the following command...
Code:
shutdown /s /f /t 0
The switches there tell the shutdown command to shutdown (/s) to force all running processes to close (/f) and to shutdown now (/t 0).