I found the same thing, HOWEVER, I have solved it. It doesn't really miss different at different distances, it's just that invisible adjustments up close, makes a MASSIVE difference at longer distances. I own only f1,2 and 1,4 lenses (for the most) where this AFMA can be a total bitch.
I have found that going +-5 steps at the time is pointless, as you can get almost any results. I for example found my 85 L front focus like nothing else at +4 but spot on at mfd, and then +5 it's dead on perfect at any distance. I never thought one step would make such a difference.
SO I have been back and forth, but all my lenses which suffered from missing way different on different distances all work at all distances now.
My 50 L looks to be quite a bit in front using the Spyder LensCal, but in real life it's dead on. So trying, in good and even light with real life subjects are extremely important. Also, indoor light for calibration is almost useless. But once calibrated properly in great light, it works in lower light also.
Just fwiw, I'm not saying no people can have an issue with their camera, but I got the same stuff, but was able to correct using real life subjects and one step at the time adjustment. It seems to get better after a +5 adjustment, but it really should be +3 for example, was hard for me to catch.