Check out this thread in LUF
http://www.l-camera-forum.com/topic/256088-s-006-focus-error/
I noticed S camera AF problem as well. Basically, it has real problems to deal with fine detail focusing subject such as small leaf, grass etc at long distance for those situation, I get very consistent AF fail. For general use, I also find reliability issue like OP report. For same subject, I don't get consistent AF results. Even for high contrast stuff(you would think), I also can get AF failure sometime. I also remember the AF system has different sensitivity to vertical or horizontal subject suggest AF point is not cross typed.
As Roger suggested, I usually just manual focus whenever I have enough time to do that. If not, I always virtually check AF before capture. for critical shot, I also make sure focus after capture. (I was burned once to find out that some of my shots from Zion was off even I though and AF point is well defined)
I have used S2 and S006 and S007. I sent my S006 to Leica just want make sure my unit is in spec. (I expect to be told it is even though I see lots of problem) In the time of sending the units. I got loan units of S2P and S007, The problem is there for every units I can hold off. The reason I know it is in spec because it can lock focus if you really give it well defend target. and I know it is in spec because I know spec is sloppy.
I was hoping S007 will improve upon this problem, but it is not. And focusing distance scale in LCD is a gimmick at best in my field use. Totally BS. For same target, I can get all kind of reading. It is not a surprise as AF doesn't know where the target is at, how can it report good results. This directly turn off all my S007 desire. I prefer 006 color anyway.
I especially hate it AF implementation of hyper focusing. I notice at small aperture, if camera detect the focusing point is within DOF window, it will not re-engage the focusing. It is really annoy that I have to Wide open the aperture to re engage the AF. This is a big flaw to me as no way the camera know what is optimized DOF window I want cover, where is my main subject I want absolutely in focus. and I think this pose a huge problem in field for me. For landscape, you will assume the lens focus at WO so that you can choose hyper focus point yourself to cover DOF. this way you can use best suitable aperture for the IQ. (S glass is capable shoot landscape WO at low light if no DOF need cover) but many case I have no idea where is the camera focusing point if it is not re engage the focusing.
For me, I don't have any other system approaching the file quality I can get from S glass and sensor combined.(I test pretty much all 35mm system) The CCD color are beautiful, 2nd to none) the OVF are the best. Shooting experience is nothing can touch it. All this overcome the flaw for me, especially I really enjoy manual focus shooting. (And AF seems works fine at portrait distance say 2~3m for 70mm, 1~2m for 35mm or 2~4m for 100mm, as DOF is bigger enough to overcome loss AF tolerance. closer than that, I mostly manual)
If you set expectation to be about AF performance of old medium format film or Digital, you will probably be fine. If you compare S to modern Canikon, you will for sure be disappointed with its performance.