Any messages you see are directly from Microsoft and are not controlled by Shavlik Protect. This document will help you configure Windows Update when using Shavlik Protect: Best Practice: Windows Automatic Updates
Basically, set Windows Update to never check for updates and set the Windows Update service to manual like you have it. Keep in mind that WSUS will show messages so you will need to either remove the WSUS agent or configure it to do nothing.
We do not recommend running Shavlik Protect and other patching produces on the same machines.
Update to discussion from Duane
We are trying to use Shavlik exclusively for patch management. The crux of the issue is, that when we set our Group Policy “Configure Automatic Updates” to disabled, Windows Update will notify our users that Windows Updates have not been checked recently. We get a blue bar across the screen horizontal with 1 button “Get Updates” If you click on “Get Updates” it takes you to Windows Update module. I would like to avoid any user notification from Windows Update but I haven’t found the secret sauce yet.
We have also tried the Group Policy “allow non-administrators to receive update notifications” to disabled but that doesn’t seem to block all notifications.
We tried stopping the Windows Update service all together but found that Shavlik used or in some way require the Windows Update service in some fashion to install Microsoft KBs.
Any other best practices to hide all notifications pertaining to Windows Update?
Please keep in mind, you never see Windows Update message when installing patch through Protect. So there is something configured on these systems, most likely through GPO, that is causing these messages. The only method of preventing all messages from Windows Update is covered in this document: Best Practice: Windows Automatic Updates Windows Update can't have any interaction with the OS otherwise it will show popups. I've performed a lot of research on this subject throughout the years and found it to be a all or nothing with Windows Update messages. That's not saying there isn't a solution, we just haven't found the secret sauce too.
Have you posted this on a Microsoft support site? (I really couldn't something searching)