This issue might be specifically for me, but I have two GTX 1080's in SLI. Well, since SLI wasn't supported by default, I looked online and found someone saying that the DarkSouls 2 settings would effectively engage SLI for Skyrim SE, so I went ahead and set it up as they suggested. After having the flashing issue for quite a while, I ended up disabling that feature, and everything stopped. So if you guys are running SLI or Crossfire, you might want to see if there is some kind of issue there.