Well, describe the noise. Does it sound like bb's in a coffee can? sandpaper?
A bearing going bad has a pretty distinct sandy sound.

As far as the flutter, when the clutch on the SC engages, the motor loses power due to the parasitic losses from the energy required to turn the supercharger. You might be feeling that but also the first time the lobes start spinning they have to pressurize all of the air between the supercharger and the intake valves. This sometimes can have a cluttery compressor surge like sound to it, since basically the supercharger is fighting this solid wall of air