I normally shoot with a 1D Mark III. I've noticed a behavior with the camera when shooting in Av exposure mode and flash, where the camera essentially dials in -1EV behind the scenes, without changing anything in the visible settings. If the flash isn't enough to light the subject/scene, I end up with a somewhat dark image. I notice it whenever I'm shooting several images and keep the shutter half-pressed - I might initially see a shutter speed of 1/125th and no lightning bolt, but when the lightning bolt shows up the shutter speed changes to 1/250th. Keep in mind that the +/- EV indicator still shows a normal exposure.
I recently rented a 5D, and never saw this phenomenon on the 5D. Now that I think about it, I may need to fire up my Rebel XTi and my girlfriend's 40D to see if it's in those cameras. Anyone know more about this, have seen it (or "definitely" have NOT seen it)?
It drives me a bit nuts, since it pushes me a stop closer to max sync speed just by turning on the flash. Since I really prefer to have the rear dial reprogrammed to act as an ISO dial, I have to go through a button-press then an EV adjustment if I want to fix this (and then undo it for non-flash shots).