it seems that the flicker is the selected animation choosing the color of the "Windows - Background" color from your current theme. the color it should be matching, i believe, is what "Controls" color scheme you may have selected.
the way to recreate this is to change the "Windows - Background" color in your Appearance Settings with the animation setting in Compiz active and you'll see that it grabs that color.
it seems that the flicker is the selected animation choosing the color of the "Windows - Background" color from your current theme. the color it should be matching, i believe, is what "Controls" color scheme you may have selected.
the way to recreate this is to change the "Windows - Background" color in your Appearance Settings with the animation setting in Compiz active and you'll see that it grabs that color.