P.S. - It is almost like a I need a second AFMA for medium range.
I've had fits with mine. The symptoms are you think you have AFMA set and you cannot get consistently sharp shots as telephoto. In fact they're rarely sharp and usually just enough off to be not quite right, with no zone of sharp focus (i.e. not a case where it just back or front focused). But interestingly it is not as much a problem using it as a macro. And when a tele shot works right, it has amazing IQ.
I finally isolated a 100% repeatable and quantifiable issue in testing. How I tested was setup tripod and test target, tether to EOS Utility, magnify 200% in EOS Utility. Then increment the focus single steps via the ">" and "<" buttons.
What I saw with my copy was that when changing the direction of focus (i.e. several ">" clicks and then a single "<" click or visa versa) the focus would change what looks like about 20 single clicks worth of going only a single direction. And not only that, the image would actually shift in the viewer frame. So something in the mechanical focus mechanism has some slop/play in it.
BTW, IS on/off doesn't make any difference in my case and I tested a friend's copy the same way and it did not exhibit this issue.
I sent it to Canon and paid over $200 and it came back the same way. I complained to them and did a video screen grab of the EOS Utility session and sent it back to them again. It should be here Tuesday and this time they took alot longer, so hopefully fixed this time.
I'll post more later this week...