This looks like some exotic issue to me. We would highly appreciate if you can sumbit a ticket to our gurus in tech support team. Please attach collector logs("Help > Export Logs" in web UI) and Operations Manager(both agent and server side) event logs to the support ticket. You can contact our support team at http://cp.veeam.com
All objects which have been already discovered (datacenters, vcenters, clusters) are in the same discovery script with ESX hosts, so it looks like some weird issue with collection or with SCOM discovery. We need more information to understand the root cause.