I had the same thing happened - on HUB/MBX server, services were enabled back, but only 2-3 of them started. I waited about 10 minutes and manually started all services. After another minute or so, setup completed successfully.
Not sure if it is related to an issue when during reboot, if one of the services doesn't start automatically, you would get error Event ID 2604 (MSExchange ADAaccess) repeatedly until you restart Active Directory Topology service (and all other Exchange services along with it). Prior to installing RU2, I rebooted Exchange MBX server and had this error in the log, since I didn't restart Active Directory Topology service. I wonder if it's related to this, since I know Exchange is very picky on how services are started, and possibly it cause services not to start automatically as they should have at the end of the RU upgrade?