Did you make sure you filled out the OU filter and Site filter correctly?
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Here is an example:
OU=Name2,OU=Name1,DC=Domain,DC=Local
Domain name is Domain.local
The first Organizational Unit is Name1
The second Organization Unit, located inside Name1 is Name2
The easiest way to make sure you have it correct, view the OU in Active directory - right click on it and select Properties. View the "Attribute Editor" tab, and find "distingushedName". You'll want your filter to match the value listed. (Just copy and paste really)
Anything in Name2 and lower will be seen and scan as indicated by the selection. Anything outside of that scope will NOT be scanned, meaning anything computers or other OU's in Name1 will not be scanned.
To add additional filters, just click the Add OU.
I do not use sites in my structure at this time, so I can't test it.
Another thing to check, make sure you have not inadvertently deployed the LsAgent to the computers specified. They would certainly be re-created/updated each time they check in.