When updating clients to Configuration Manager 2012 R2 CU3, there will be a notfication in the tray telling the user that something is installing. This can sometimes be a bit confusing for the user which can result in unnecessary support calls. In my opinion, the user does not need to see these kind of notifications, so the CU3 update should be installed silently.

This is how you do it:

1. Go to the CU3 package created by the CU3 Wizard and select the update you want to install silently.
2. Open Properties for the Program and select Run: Hidden
4. Check the checkbox “Suppress all program notifications”