FWIW, I have a lot of problems running SetCPU on BBv1.1 on the 1.0 GHZ Kernel.
SetCPU with profiles set up will randomly show (and then lock on) 384 MHz. I can only get back to 1.0 GHz by resetting the Droid. In addition, I have had times where with SetCPU running, I will feel the battery getting hot when the phone is not under any load - I need to reset the phone to get the battery down to more normal temperature.
I have also seen BBv1.1 get the battery very hot under no load with SetCPU uninstalled. This sometimes happens just after the phone boots.
I didn't see any of these issues with BBv1.0