thats like mine, the lights go off over night and thatswhen the spot disappears, then after the light being on for a bit it comes back super jet black!
I've not noticed this in my Guppy specifically but I certainly can attest that colorations fade dramatically when the lights are off and come back within 5-10 minutes after the lights are on. This fenom happens most dramatically in my tetras (high-skirts and neons) - I will chekc out the guppies over the next couple of days.
I honestly think this happens when they sleep. I know this doesn't speak to the gavid spot in your guppy, but I could easily see this being related. Of course I'm only speculating here.
FYI - My guppy is in the Birthing Tank...AGAIN!!! I will try and get some pics for comparisons