Here is an article from the OpsMgr Engineering Blog detailing an issue with SCOM discovering Ckuster Resources

“If a Cluster has orphaned object entries in ClusterHive registry key, the System Center Operations Manager agent may not discover some or all Cluster resources. This can occur with System Center Operations Manager 2007 (OpsMgr 2007) or System Center 2012 Operations Manager (OpsMgr 2012).”

The article details a fix which envolves locating and then removing the orphaned objects:

“First, use the Failover Cluster PowerShell commands Get-ClusterResource and Get-ClusterGroup to get the list of Resources and Groups. Then, using the output, check for Resources/Groups that appear as Offline and verify if these can be seen in the Failover Cluster Console. Verify with the Cluster administrator whether these are still valid, then assuming they are not and you’ve identified which ones that are orphaned, delete them using these commands from an elevated CMD Prompt (Run As Administrator):

For orphaned resources: Cluster RES “<RESOURCE_NAME>” /DELETE

For orphaned groups: Cluster GROUP “<GROUP_NAME>” /DELETE

Once this is done the missing cluster resources should now be discovered.”