Derek - a couple of questions. How does the camera know whether you are using the flash as your primary light source, or if you want it 'to properly expose the scene with ambient light'? Secondly, I don't understand how you can set the camera up in exactly the same way in 'M'.
The camera will always assume that ambient is your main source of light. IN AV, if you set f/5.6 the camera will adjust your shutter speed to get a proper exposure. Let's say that it comes up with a SS of 1/60s. So you are shooting and 1/60s and f/5.6, ISO 400. Now you turn on your flash and it "fills" in the shadows. The camera and flash should behave exactly the same if you set your camera on M and dial in 1/60s and f5.6, ISO 400 and use the flash. This is all assuming ETTL of course. For fill flash I personally set my FEC to around -2. If you leave it around 0 and your subject moves, you will get ghosting since the ambient and flash are exposing nearly equally.
You need to tell your camera that you want the flash to be the primary light source. With my settings above and in M, I would simply set my shutter speed to 1/250s This would mean that my ambient would now be underexposed by 2 stops. I then make sure my flash's FEC is set around 0. This is "telling" the camera that I want the flash to be the brightest light source, and that I am not concerned with letting the ambient light be responsible for exposure. My camera's meter should be at -2.
In AV mode, all I would need to do is set the camera's EC to -2, and leave the flash set around 0. this would in effect do the same as I did in M by underexposing the ambient and keeping the flash up around proper exposure.
This is of course a simplified explanation, and there are a ton of different ways to go about it. 

