I bought it when it first came out a year ago, and each new version has worked better than the previous. Sure, there are a few minor bugs, but most of the time, the issues have been mine.
Correct setup, plenty of bright light, absolutely no vibration or movement, concrete floor is far better than a wooden one.
Some lenses are problem lenses, they just do not perform repeatedly or well. In some cases, its the lens design, the cheap 50mm lenses are never going to do well. The "L" lenses do very well.
I've found that the 5D MK III gives much better results than my 5D MK II's did, and that is borne out by the data sent in from testers.
If your setup is perfect - stable, bright light, viewfinder blocked, firm floor with no vibration, accurate target alignment, then AF issues are likely a problem camera or problem lens. Both can be problems, we just never had a way to test before.
Overall, it works well and is repeatable for me, but the devil is in the details of a good setup.
As far as computer issues, I've had none on my Lenovo Windows 7 64 bit laptop or old Dell XPS-420 desktop that was upgraded to Windows 7 64 bit. Having a lot of older equipment increases the probability of drivers conflicting, or software conflicts. Those just have to be worked thru, there is a infinite number of combinations of hardware and software, so no amount of testing will guarantee that it works for everyone. I'm now in the process of testing out my new Dell XPS 8500 with Windows 8 64 bit. FoCal is installed and running fine, but I've not done a full AFMA using it. I most likely will not in the near future.