Hello Auhn,
what`s your configuration for "Display a temporary notification to the user that indicates the interval before the user is logged off or computer restarts"?
Check this post https://social.technet.microsoft.com/Forums/en-US/cc03f9f6-dcdb-4096-a115-f42b2ba348b8/windows-updates-not-running-even-when-maintenance-available?forum=configmanagersecurity
Ans also here is an excellent Post about maintenance windows:
http://blogs.technet.com/b/server-cloud/archive/2012/03/28/business-hours-vs-maintenance-windows-with-system-center-2012-configuration-manager.aspx
cheers
Jakob