I have this problem too, though it seems like only some of the time -- I'll have to look at that more closely. Honestly, I don't pay enough attention to say if it's always or just sometimes. But I most definitely have noted the really dark portraits at times.
Also, something which may be related -- the images saved with saved costumes are very dark. So much that I cannot differentiate some of them at all. Very dark and washed-out looking. Similar to the way the dark team portraits look, really.
Believe this is an issue of lighting not being applied properly when the 3D image is converted to a 2D texture.