The Configuration Task from the SCOM Console executed successfully without the slightest error?
You checked also the configuration from the SharepointMP.config and it matched the run as account (if there is none configured SCOM will run it with the default action account) + the all SharePoint Servers are configured correctly.
There is no sharepoint server in the unidentified machine state?
Also no discovery scripts on the sharepoint agent side, nowhere to be found like
What to check next:
Powershell V3 should be uninstalled by removing the KB above for Windows Server 2008 R2 SP1
KB2506146 (Windows Server 2008 SP2) because it is unsupported!
2. Check if there is any powershell version installed. The Windows Server 2008 OS usually doesn`t ship with powershell installed, as does R2. SharePoint discovery needs powershell version 2.0 installed.
3. Check the powershell path! In some cases, even if powershell appears to be correctly installed, SCOM executes all scripts using the PSModule Path from the environmental variables. Make sure the path matches your powershell executable location.