FYI - I stopped the Forefront controller service (which stopped all Forefront services) and ran the update to SP1 RU6, when the server came back up the Forefront services were NOT started and when I started the Forefront console it complained about not being hooked into the store with the error "The MS Information Store is running but the Forefront VSAPI Library is not registered."
I followed the steps in social.technet.microsoft.com/.../58f712ae-e141-4010-b8c8-0e0c4eab9d3e and got it hooked back in. This happened on multiple servers, and was consistent.
When I didn't stop the Forefront services before hand, RU6 applied fine and everything was 100% happy post reboot. The moral of this story is to ignore the recommendation of stopping the Forefront services and to just plan on rebooting the server after installing RU6. Really rebooting isn't a horrible thing if you are taking down all of the Exchange services anyway - you might as well reboot.