It looks like version 6.4.1.0 of the SQL 2012 MP broke discovery of AlwaysOn (the AlwaysOn Seed). The old version had this for the registry key (note the bit in red, it's missing from the new one):

SOFTWARE\Microsoft\Microsoft SQL Server\MSSQL11.$Target/Property[Type="SQLServer!Microsoft.SQLServer.ServerRole"]/InstanceName$\MSSQLServer\HADR\HADR_Enabled

And then this is 6.4.1.0:

SOFTWARE\Microsoft\Microsoft SQL Server\$Target/Property[Type="SQLServer!Microsoft.SQLServer.DBEngine"]/InstanceID$\MSSQLServer\HADR\HADR_Enabled

The discovery works fine for our management group that's using the old version, but it's not working for our MG using the new version. Is anyone else running into this?

Hi,

SQL Server Management Pack version 6.4.0.0 improves performance of AlwaysOn discovery.

Appendix: AlwaysOn Management Pack Contents
http://technet.microsoft.com/en-us/library/dn456931.aspx

Please ensure your Management Server with latest update installed. Also check if there is any related event.