Thanks for posting!  Cluster support happened relatively recently, so having the latest OMSA and IT Assistant is a good first step.  I suggest making sure that your discovery ranges do include the IP addresses for the physical systems, but not the virtual IP for the cluster.  That will most likely get them to discover correctly.
Is there a best practice for discovery of Microsoft clusters (both 2003 MSCS and 2008 Failover) within IT Assistant?  Perhaps something documented that I missed... It seems that sometimes they discover properly, including physical node names and cluster name, and show up under correctly in 'HA Clusters'. Other times the physical node appears with the cluster's name.  I've tried removing all associated entries and running an inventory; checked DNS; checked SNMP and checked Server Administrator.  The one thing I'll mention is that not all servers are on the latest version of Server Administrator... some go back to 5.5  But does it make a difference?  
IT Assistant 8.6 and Microsoft clusters (MSCS and 2008 Failover)