I consider myself somewhat of a Gameface expert.
First, transferring to Madden 13 is terrible - the models just can't handle it. Hopefully they get this fixed in '14.
Secondly, your skin tone is taken by the color of your neck. I had the orange problem too and you can actually go into photoshop, crop your neck and just fill in a solid color of skin tone you desire. Then make sure the neck dot is in that place you photoshopped.
Problem fixed
But still it'll keep you angry when you import to madden, hardly any of the hairstyles work. You can't even get a bald or buzzed haircut. I spent hours trying.