Creampuff an Paulusje, you give valid comments (although the focusing screen needs to be aligned with the sensor for manual focusing to be accurate, if one wants to be picky, which will of course mean that it is also aligned with the AF sensor if the AF sensor is properly adjusted). However, I think that you have misunderstood the question. The OP stated that manual focusing works very well with the screen, but that he has problems using the focus indicator of the camera (when the red focus square flashes when something is in focus, and the green hexagon lights up). In other words, the OP has most likely succeeded in adjusting the focusing screen correctly.
The AF system (which is what triggers the indicator) should be independent of the focusing screen, just like Creampuff mentioned. My guess is that what you are experiencing, Atekant, is seeing a pattern where there is none. Humans are extremely good at this -- our brains seem to love finding correlations and patterns even when they do not exist. If that is not the case (in other words, something really did change), then something has happened to the AF system. Possible changes: you shoot different subjects, have different lighting, have changed your focusing technique (likely without thinking about it) -- e.g., maybe you tend to turn the focus ever so little more or less now before you stop compared to before when you see the indicator. There is a tiny interval of the indicator, and focusing with it can be effected somewhat by the user. It is also possible that you have just seen statistical variation, and that the difference would disappear with a larger number of tests. There is also the possibility of the placebo effect (seeing what you want or expect to see). This effect should not be underestimated.
I may very well be wrong, and I do not know how stringent your tests were, but I have seen all of the above effects many times -- both in myself and others -- and it amazes me how powerful they can be.
EDIT: it seems that I, too, was a bit quick in reading the question, and I missed the last part. The focusing screen should only be adjusted to the sensor. If you would re-align the screen (re-shim it) to match the AF indicator, you would set the screen off-focus. There is no way to adjust for that with the camera focus adjustment. If the screen focus properly as it is, it is at its correct setting and should not be changed. From your description, I would make a system-wide AF adjustment for the camera (leaving the screen as it is), to have the focus indicator match the screen. After that, you would have to adjust all of your individual settings for different lenses, IF those two settings are cumulative (combined). If they are not cumulative, you would not need to change the individual settings. I do not know which way it is, so just try or maybe someone can enlighten us. I would guess that if they are cumulative, you could just subtract from the individual lenses' adjustments what you add to the global adjustment (or vice versa).
Last edited by hjb981; 06-25-2012 at 08:35 AM.