Hi Ari W._
Do other updates have the same issue that report as "not applicable" while they are "applicable" for clients?
Please check the report time of the clients, verify if the clients report to the WSUS sever after syncing WMF 5.0.
Also reset windows update components on one of the test client, check if it could help:
https://support.microsoft.com/en-us/kb/971058
Best Regards,
Anne
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