I logged on to the latest snapshot, 15w47a, and my black skin overlay (Left and right arm, right and left leg, hat and jacket) dotted around my skin had become transparent.

Just also found out, i go in my inventory and the skin layer is black again, when I give myself my head, the head overlay is black, when I place down my head, the overlay is black, when I wear my head in 3rd person the whole head goes transparent and when I stand in 3rd person next to my head placed down the head on the ground is transparent, when on an armor stand and wearing the skull the head on the armor stant is transparent, and the armor stand is broken and just now, my skin went fully transparent. My skin is completely broken now.

Added a few screenshots to help understand.