Are you attempting to back up the SQL VMs as VMs? Instead of doing that, because the virtual agent doesn't know that they are clustered, back up the resource by it's Cluster name. You need to install the Backup Exec Agent on all the nodes of the SQL ...
You are correct, installing BE16 should have resolved this issue. If you are seeing this, then you should open a support ticket along with the technote so that it can be fixed.