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Do you have Software Distribution enabled in your patch scan template that you're using in Protect?
What kind of results do you get if you run a scan in Protect using one of the built in scan templates? (Security Patch Scan or WUscan)
This document may also be helpful for this scenario:
No. I have created a new patch scan template to make sure there were no strange settings but it is now coming back saying there 25 patches missing.
The scan template looks like this:
Product filter: scan all
Patch filter: scan all
Patch properties: Scan selected (security + Non-security)
Criticality filter: Critical + High
The general tab is to only scan for missing patches, software distribution is disabled.
A security scan comes back with 7 patches missing.
A WU Scan comes back with 25 patches missing.
I'll have a look at that document just now.
I'd suggest removing the criticality filter settings unless you have actually gone through and marked patches with custom criticality. This setting is actually just for custom set criticality - it is not based on the vendor severity. If you have it set to use these custom criticality filters but haven't actually gone through and marked custom criticality settings on patches within Protect it can cause odd scan results.
I hope that helps.