The messages you or the users are seeing would be coming from Windows Update. We recommend if you are using Protect to patch your machines that you turn off windows automatic updates on client systems. Shavlik Protect doesn't interfere with Windows Update if it's enabled. If you need a way to disable windows update from the registry, it appears there are some directions out there. Here is one article from Microsoft that covers it - How to configure automatic updates by using Group Policy or registry settings.
Just make sure you don't disable the Windows Update Service - this is still needed to run many updates and needs to be set to at least 'Manual' start-up type.
I hope this helps.
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I was having the same issue and have to change my Group Policy Settings. At the same time you might want to delete you C:\Windows\SoftwareDistribution folder as it will contain all the previously downloaded and not installed Windows Updates. In some cases this can be a significant amount of space especially when some companies use smaller C:\ sizes. You'll need to stop the "Windows Update" service before you are able to delete the folder. And don't worry, once the service starts again, it will automatically recreate that folder.