@seancass35
You should also change the entries for the Dynamic Shadow Fix:
Dynamic Shadow Fix
Use the following Bioengine.ini tweaks:
Find the following entries:
DepthBias=0.030000 or(0.012 if you restored to pre-official 1.2 patch values)
MinShadowResolution=32
MaxShadowResolution=512
ShadowFilterQualityBias=0
And change them to:
DepthBias=0.006000
MinShadowResolution=32
MaxShadowResolution=4096
ShadowFilterQualityBias=4
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Apart from that, do you use a 64bit Windows?
Do you use SweetFX or a similar tool?
The only interaction between Afterburner and the game would be the overlay (FPS) from RivaTuner. You can test this easily by shutting down afterburner and test afterwards.
Still, overclocking the GPU could cause such problems too, so if you overclock set the GPU back to the factory settings to make sure.
Did you tested the Game with a standard BioEngine.ini?