Can AF be off in a camera – rather than a lens?
Re: Secondary optical path to AF sensors
It sounds very odd - I know it can be the camera though - before upgrading to the 6D, I owned a second hand 5D classic - on most of my lenses the focus was out, it was painful knowing I couldn't do anything about it without having to take it to a shop (I never did). But now with my 6D, most of my lenses focussed perfectly without any micro adjustments! It makes no sense because some were way out and others were pretty good.
I hope your issue can be resolved - but from the sounds of it - if I were you I'd just manually adjust the micro focus and test it until it seems about right (I didn't bother with any charts, just a bag with a rough stitching and a marker.