I feel the same way, but about having hair... when I see a picture of me (bald on top, but before I shaved my head, and with a goatee) I really have a strange, uncomfortable feeling. How could I ever have thought that was a good idea?!
And now, as I begin to transition, I see more and more of the person I have always been peeking out through the eyes in recent photographs... my eyes are more alive, the shadows and haunted look (even in my goofy face photographs) are dissipating...
I think as we accept ourselves, and start to transition, there are visible clues that we pick up on. We recognize the misery in ourselves that there was before, perhaps. Yes, it makes me uncomfortable... kind of like looking into the haunting eyes of a suffering stranger in a photograph... with the added realization that the suffering was in *me*.