I purchased the same lens early this year, and experienced a handful of nuisance issues, which caused me to return the lens for a new one. One of those issues was consistent focus, and AFMA not having enough range to correct it.
The first lens was a loose fit. You could actually hear a clicking noise. After receiving a new lens, I realized the issue with the first had been a missing rubber ring on the mount for weather sealing.
My second lens didn't seem to focus accurately, or consistently, with the AFMA tests. I have since learned that my initial tests may have been somewhat flawed. I was performing the tests indoor, in a sufficienty large room, because it was winter outside. I typically ran the tests several times on a given lens, and took the average as the final setting.
After retesting outdoors once the weather warmed up, I was able to get very consistent results. Not only that, but my results were well within the adjustment range of the AFMA, where previously I had been pushing the edge of the adjustment range. I was using the Dot-Tune Method.
Doing a little more research into the entire AFMA procedures, I learned that ambient light can play a significant role in achieving consistent focus during the tests. Most types of indoor artificial lighting [mine were your typical commercial office flourescent] can cause the camera/lens to focus inconsistently.
My EOS 6D did not have a light flicker adjustment on it. But, if you perform your tests indoors with the types of lights that flicker at line voltage frequencies, then I suggest that you re-test your lenses with the flicker adjustment active.
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