I have just started getting this as well. New computer with 8800GT, fresh install of SH3 and GWX2. Using 16km, 3d waves. Noticeable flashed black boxes when the weather is good

, but not when it rains...
On my old PC with 9800XT and GWX1.3 at 8km I did not see this. Need to experiment more as I'm new (again) to Nvidia.