I had a shutter mechanism fail at 20k frames... they're mechanical parts, bound to have failures of some type, it's just the law of averages, they can't be perfect...
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Regarding the 1DX (I'd guess it's the same for the 5D3 having the issue too...), send it into Canon for inspection... just got mine back from CPS, shutter assembly had to be replaced.
I had an under-exposure issue on the first frame vs. your darker... shutter was sticking for the first exposure then was fine for subsequent frames. Mine would occur after the camera had "rested" for awhile, as long as I kept using it I had no issue, it was the first burst after not using the camera for a bit. I noticed it happening the first burst of the day, I was shooting a 22 day baseball tournament so I got to see it happen and could recreate it quite easily.
You describe my problem. Many thanks. Canon has to fix this with a replacement of the shutter assembly.
1Dx RAW files are better. Don't know why. I had a 1Dx and a 5D3 and sold the 5D3 and got another 1Dx. You'll love it.
With the latest FW there is a way to have both AI Servo and One-shot modes programmed to two different back-button focus buttons. I have my Af-On button as my regular AI Servo mode and I have the * button set to be one shot focus. This setting is done differently than the way you are doing with the AIServo-Oneshot switching button, which as you have found out requires it to be held down. With the other way you have a full separate button for one-shot and a separate button for servo.
You set this up in the C.Fn 5 menu under Custom Controls. You would set the shutter button to "Metering Start" and then you would set AF-On and * to "Metering and AF start", select it and then press the INFO button for the "Detail Set". This will give you a menu with 4 options: AF start point, AI servo AF characteristics, AF mode and 14FPS super high speed mode. You only need to make changes to the * button as the AF-On will stay at default values. For the * button I go under "AF mode" and select "ONE SHOT".
Alternatively you could use this way to set up two different AI Servo modes on the two different buttons.