sadly i think there is no solution to that
its a bug of some sort, either in il2 itself or in the gfx card drivers. afaik nobody has ever been able to solve it (and by the time people started reporting it to oleg he was already working on BoB, so wasnt investing time in further bug fixes in the old game)
the only practical sugestion i have to reduce the irritation from the flikkering caused by the flashing box is to temporarily cover that part of the 3e monitor with something that hides the flikkering while you are playing il2. sad but true