This is a common area of confusion. The camera is actually behaving in an ideal way but if you haven't been shooting flash for years you might not guess why it does this.
When you meter with flash, the camera mostly ignores the flash. The light meter performs metering for the available light only.
When using E-TTL (really E-TTL II), the computer in the camera calulates the amount of power needed to adequately light the subject based on your exposure settings... but ignoring the shutter speed (so it really only cares about ISO and aperture... well, it needs to make sure the shutter speed is within the "flash sync" range unless the flash has high-speed sync enabled.)
This is because while the available light is more or less "continuous", the flash is a momentary source of light. The camera needs to use a shutter speed at or below the camera's "flash sync" speed (which varies by camera and is typically in the range of 1/160th to 1/250th sec). The max "flash sync" speed is based on the amount of time needed for the mechanical focal plane shutter to completely slide open, allow the flash to fire, and then completely slide shut. The need to operate this way is based on the design of the focal plane shutter. The shutter uses two doors or "curtains". One slides open... the other follows later and slides shut. If there were only one "curtain" then pixels near one edge of the sensor (where it starts to open) would technically get more light then the opposite edge of the sensor ... because the "curtain" would have to reverse. By using two "curtains" and having them both travel in the same direction, all pixels technically are exposed for the same amount of time.
The amount of time that the flash is illuminated is usually extremely brief. It varies by flash model and also the power level -- but it could be as brief as 1/4000th sec... but regardless of how brief it lasts, it can fire until the shutter is completely open or part of the sensor will have it's light blocked.
Ultimately this means that if you use an extra long shutter exposure (e.g. suppose you set the exposure for a full 1 second), the flash will fire... (let's say it lasts 1/1000th sec) -- but leaving the shutter open longer will not actually increase the amount of light recevied by the flash, because now the flash has gone dark.
That extra long exposure time WILL improve the camera's ability to collect more ambient light even though it will not collect more light from the flash. When you use flash, you start to think of each shot as two different exposures... an exposure for the "available" light and an exposure for the "flash". Changing aperture or ISO settings affects both equally... but changing the shutter speed only affects the "available light" part of the exposure because the flash is a momentary source of light.
Suppose you are in a room with low light... you take a shot with flash. If the camera ONLY exposes for flash, then your subject is illuminated, but everything else in the room appears to be nearly black and the shot doesn't look very good. But if you leave the shutter open longer then the camera can collect more of the available light and the lighting will look better -- you'll have some balance and depth to the shot because you'll be able to see the background. This technique of leaving the shutter open longer is called "dragging the shutter" and it makes for better flash photography.
This is one key reason why you'd want your camera to meter for available light even when it's using flash.
The other reason is for daytime shots. I use flash to shoot outdoors during the daytime (it's actually one of the best times to use a pop-up flash). This is referred to as "fill flash". The idea is that the sun is lighting your subject, but the flash is filling in some of the deepest shadows so they don't look so harsh. You don't want the flash to try to compete with the sun. So you can set the flash exposure compesnation to -1 and take the shot. You do similar things if the subject is in shade but the background is in sun -- to balance the lighting between subject and background.
Tim Campbell
5D III, 5D IV, 60Da
