16/4 isn't optimal, not sure how much a 4x would hold back a 6850 but still. As for the temps, is there room between the cards? Do you have good case airflow - that's really important when you put more heat-generating components in there.
You could try swapping the cards, but if they both have decent coolers odds are the temps will just swap so the new top card is running hot.
CPU bottlenecking shouldn't cause negative crossfire scaling, but of course it could cause disappointing performance otherwise.