Several others things to be aware of:
1) The focus adjustment is for AF, not MF. While it might also affect the focus confirmation, I wouldn't count on it - no one really knows exactly what it does. Chances are pretty good it really doesn't affect the detection of focus, but rather, the mechanics of turning the focus ring (or the SDm equivalent).
2) The actual focus sensor is much bigger than the little red square. So the square might light up in one place but it might actually be focusing somewhere a bit different. It's giving a general idea of where the focus was detected, no more. If you're trying to focus that specifically, you cann't depend on the confirmation.
3) Even at f/2.8, DOF can be shallower than what appears in the viewfinder, enough that something can appear in focus in the viewfinder but not be in focus in the picture. That's just a fact of life with the Pentax focus screen, which has a minimum DOF it is capable of displaying.
Quote: My old DS2 nailed the focus with the same lenses.
Probably not with the exact same test - the problem is probably with the test, not the cameras or lenses. Your test includes too much stuff at different distances all within the rather large area covered by the focus sensor.