Had the same with our current SGS4442, which replaced an older Bosch model which used to clean everything perfectly! The Bosch service agents had it for a week for testing before returning it, declaring that it was working as it should be and advising to use the Finish 'Powerball' tablets.
It still left puddles of dirty water in the concave surfaces of upturned cups etc, and as you say, the sump water is pretty filthy, so it's performing the final rinse with dirty water! It seems to be all part of the drive to design appliances to consume less water, so the problem probably won't go away with successive designs either.
To combat the problem I put the machine through a rinse cycle first, before the main wash. This obviously consumes more water (and electricity), but at least most of the muck is washed away first before the machine commences the main wash, with what will now be cleaner water. I have found that the sump water remains much cleaner now, with no dirty puddles on upturned cups!
Hope this helps.
Nigel, March 2007