It looks like this issue is somehow connected to adjusting brightness. When adjusting brightness in TF2 it happens, but when running TF2 with the -autoconfig switch and then adjusting resolution + other settings except brightness it runs without any of the flickering !!!
So it looks like the brightness value is only adjusted on one of the cards hence the flickering in dark areas.
This should be something ATI could fix with a new driver or game developers could avoid by programming brightness a certain way, since not all games show this behavior.
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