Auto exposure not applying when using the auto enhance function

I am on Aperture 3.6 and Yosemite. I use a Canon 6D and shoot in RAW. When I am doing the batch auto enhance to my shots, I find that even though in the adjustments preset Auto Enhance includes auto exposure, often it is actually not applied. Are there anyways to fix this? The images actually are a bit underexposed and I now need to go through picture by picture to click on the auto button under adjustment. Thanks.

Have you set your camera to use Canon's Highlight Tone Priority? Then most of the Raw files will be underexposed, because Aperture is developing the RAW file "as is" and not applying the in-camera settings. See Keith Barkley's user tip.
The Big Three: Setting your camera for the best Aperture RAW results

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