Joe and Christina, I've just checked the instruction manual for my Canon 60D to see how to set exposure compensation when shooting in manual and with auto ISO. It's not possible. I'm not sure if this is true with more expensive Canons but exposure compensation can be used with auto ISO only when shooting in aperture priority, shutter priority and P. I take it from your discussion that exposure comepensation can be used on Nikons when shooting in manual?
P.S. My wife and I are visiting a raptor centre tomorrow so I'm hoping for a few shots.