Mom2005 agent for FCS v1 can slow boot times by around 20 seconds (typically)...So I did a WDRAP recently where part of their slow boot experience was related to FCS. It's not FCS's fault though, it rides on top of the old MOM 2005 health agent. Oddly enough, the MOM 2005 health agent, in the registry called:
HKEY_LOCAL_MACHINE\Software\Mission Critical Software\OnePoint
Has a value....
Where, at my customers site, the X was 60 (value is in seconds by the way).
Flipping that bit to 0 increased their overall boot time by about 18-20 seconds. Not a BIG deal, but, a deal nonetheless. I've done some research on this and no impact has been seen by setting this to 0 so far at any customer....
Another fix would be to check dependencies of the MOM 2005 Agent with the Service Control Manager, ala http://msdn.microsoft.com/en-us/library/ms681957(VS.85).aspx. As the basic problem is that MOM blocks the service control agent while it runs through it's boot delay.
But, I found it easier to flip a bit in the registry from 60 to 0 myself...chances are you will too.