This is the same effect as the one in my recent level Stormy Day. Use this sample in your levels if you want.

Tutorial:

Step 1: Download this addin

Step 2: Go into your level and import white32

Step 3: Change its animation to StormFlash

Step 4: Scale the image to cover your whole level, change the depth to 30 and move below your level.

Step 5: When you export into a goomod open the goomod with WinRAR or 7zip and in override/res make a folder called anim and drag and drop both storm flash files in your anim folder.

That is it. Let me know what you think