Originally posted by PushTheRedButton I checked, and I did have it set to link AE to AF point, but could the flock of birds that far away really make that huge of a difference?
Should not be the cause of the exposure difference here, since your example pictures show the same aperture, exposure time and ISO values. All any exposure automatic does is adjust those three values; you can have one (T or Av with ISO range), two (T or AV with fixed ISO, TAv with ISO range) or all three (M) values locked down, and the camera will adjust the ones that are not locked (none in M). Even exposure compensation doesn't change this, it just adjusts the measurement taken by the exposure meter for your selected metering method in one or the other direction.
Originally posted by PushTheRedButton edit: The raw photos didn't upload. Gonna try again.
edit 2: my raw files are "invalid" (DNG)
You can't upload RAW files here, you'll have to upload them elsewhere (e.g. Dropbox) and link where they are.
Originally posted by PushTheRedButton So here's why I'm confused about that. Shooting at f/2.8 will leave the lens wide open and the blades are as far apart as they can be. The more the lens is stopped down the close the blades come together, so to speak. Maybe you can explain a little more because I would think the opposite would occur.
Go into M mode, select an exposure time of a second and set the aperture at around f/16. Look into the front of your lens, press the shutter button and watch. The physical aperture (the hole created by the aperture blades) should go from wide open before you pressed the shutter button, to closed down almost completely for the one second after you pressed the shutter button, and wide open again when the shot is done. (there's also a button for optical preview on some bodies or you could assign a button to trigger the optical preview; it will stop down the aperture to the chosen value (make the hole smaller) for as long as you hold down that button)
This is done so that the camera can use all the light that comes in through a larger aperture (smaller value, like f/2.8) to more accurately focus and meter the scene, and it also allows you to see the scene brighter in your viewfinder than it would be with the lens stopped down.
The camera only stops down the lens right before the shot. When you take multiple images in a short burst, the aperture in the lens may not be fast enough to stop down all the way it should in time for the image, and that's what some people already suggested here and that's what I also think might be causing the difference in exposure here despite showing the exact same exposure values.