@ayshih: Thanks for your reply.
The 60D hast no AF configuration, that is one missing feature to the 50D, propably to make a bigger difference to the 7D at this time.
I use the 70-200 IS II.
I tried it again, the values in the original Canon menu are the same as in the DotTune module menu, vice versa - so this works.
I tried with -20 to 20 manual and with the option "all lenses" instead of "this lens" - this seems to be the problem. "all lens"es works fine. There might be a problem, that its a zoom lens? In the Canon menu I got two values W and T (Wide and Tele it seems), but the one value in the DotTune module seems to stores to both settings (propably ok), but I again get these problems, that I even get at -100 and +100 a focus indication.
Anyway, no matter... I can use the "all lens" option and remember the values at 70mm and 200mm (and other lenses) and can store these manually with the original Canon menu. It is a big hit.... but "unfortunately" my 70-200 after the test want to set a "0" value - and this seems ok - because this lens IS very sharp - i never had problems with it. ;-)