On upgrading from 5.x to 6.1, my instance monitoring stopped being able to gather the objects list, or query plan information.
(SQL Server monitoring).
After a few days to see if I was impatient (this is in testing), I finally had to delete my server instance configuration and start over. Within a few minutes the newly configured instance was gathering both items.
Note: I have not enabled OS statistics gathering, so I do not know if that broke in the upgrade.