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Could be a couple of things, so to help find out what it might be, I would do this:
Find a test machine that isn't showing up, click Check for Updates, and see what happens.
- If it shows up, then I would wait. Let your machines work it out with WSUS. Maybe kick it off so they all check in or if you've got a scheduled update, wait for the results of that.
- If it doesn't show up, hopefully it gives you an error which you would be able to troubleshoot.
Especially when starting out you will want to verify pre-requisites and configuration. Patch Manager only really needs three things to be in place for managing third party updates (Group Policy-wise):
The rest of the policies there are your preference.
If you get an error code from Windows Update: