I assume this is Windows because you mentioned Windows Update, but which Windows and what make and model computer?
It's difficult to diagnose this problem because all programs have to be closed, but there is always something running in the background and the shutdown procedure should end those. But determining which one is failing is tricky.
Try this. Next time it happens make a note of the time before hitting Shutdown. Then the next time you reboot, head over to the Event Viewer and look under both the Application log and the System log to see what is taking time to shut down. You use the date/time column to work out where the block is.
This has never happened to me before, but this started to happen a lot more often.