Can confirm with 15w49a
So, they are only just enough to go over the hats? That is a feature.
I'm having this problem too. It only started happening in the pre-releases, though.
This is happening to me too, but it only started happening for me in the pre-releases. I thought it had something to do with my arms being skinny, but my hat layers are still gone!
Also, on the player heads, my 3d hair is there regardless!
Also, I've just put my skin back to my 1.7 one, and my hats are back!
And all my 2nd, "hat" texture layers are missing. I now look very weird...
Personally, I like the original. I think the fixed version is too noticeable, and it doesn't give that much information, anyway. Also, I've never experienced having to squint in order to see it. I also like the original one because it looks dirty, as if a used tool, rather than some arbitrary bright colours that people have learnt to associate with traffic lights, and I especially don't like the yellow, which from memory is supposed to be the most noticeable colour to humans or something. The yellow stands out way more than the other colours, especially the red which is the most important one to pay attention to.
That's just my two cents though.