Originally posted by sTi I think there are two possible problems here at work:
[LIST=1][*]PDAF sensors cannot see how the focus actually is at f/1.8. Older cameras like K-5 have f/5.6 AF sensors, newer like K-5 II and K-3 have f/2.8 sensors (at least in the centre). If the lens in question exhibits focus shift (point of perfect focus shifts when stopping down) the camera has to guess where the focus will be at 1.8. The LensROM may(!) contain focus adjustment offsets that tell the camera in which direction and how far to compensate the focus to work around this problem based on the aperture used. I am not entirely sure, but I think if such a problem were present it would show itself in wrong (but consistent) focus.
Your idea intrigued me. Could our camera bodies be having trouble with f1.8 lenses, such as the Sigma? So, I was interested to run some tests (I've just begun) to see how well my copy of the 18-35mm performs as aperture changes. I chose a bright blue trashcan about 10-12 feet away, with large white writing on it, something easy to focus on. I set up my K-5iis on a tripod with 2 sec delay and took a series of shots using 18mm, then 24mm, and then 35mm. In most cases I refocused between shots; a few times I kept existing focus between shots. At each focal length, I took a shot at f5.6 and at f8; and for each of these two shots, I first focused using PDAF (2 shots), then CFAF using LiveView (2 shots), then manual focus (2 shots). Then, staying at 35mm (for easiest focusing), taking single shots, I opened up to f1.8, then to f2.5, then to f2.8, then to f4, then again to f2.8, f2.5, f2.2, f2, and f1.8. At f2 and f1.8 I took a shot using PDAF and another using CDAF. Then using PDAF I kept f1.8 and went from 35mm to 24mm to 18mm.
Results: in the series at f5.6 and f8, generally the camera focused well using any of the three focusing methods. There were one or two shots that were soft, either due to focusing inconsistency or perhaps my error. Interestingly, moving from f8 to f1.8 produced the worst focused shot of all. And focus stayed poor (though a bit better) from f1.8 through f2.8. But at f4 it was very sharp. Here I wondered if your idea was correct. But then I went from f4 down the list to f1.8, and shots stayed sharp down to f2. The PDAF shot at f1.8 was out of focus, but the CDAF shot at f1.8 was in focus. The last few f1.8 shots using different focal lengths were all in focus.
I'll try another set of shots later to exclude some more possibilities. For example, I'll refocus between each shot, I'll try only PDAF going up and down the apertures, etc.