I think it's because the face texture may be inside the transparent shape.
Hold on...
Are you sure you exported the transparent thing correctly?
From what I'm seeing here the transparent thing also hides the ground texture, which is obviously not supposed to happen.
EDIT: Try setting all your shapes to detail100, the default playermodel is like that.
2EDIT: Also, last time I tried .ifl's everyone crashed whenever I used custom decals/faces. Pretty sure Badspot didn't add custom .ifl's to loadstream or something.