I use a 60D, at clubs I will go manual with my 30mm sigma, set the lowest shutter I can handhold comfortably, nice low aperture and let auto ISO do its thing. It works exactly how it should going from 100 to 3200 (locked at 3200) to obtain proper exposure. I would much rather use a flash but I don't always carry everything.
Auto ISO with a flash mounted wont go above 400 but it should drop to 100 if enough light is available. If you want higher ISO with a flash manual is the only way I know.

