Hey Zarxrax,
The edges need to be antialiased against something. Normally it is done with transparent, but since only one color can be transparent with a gif, there needs to be some color in there. With the skins, I am going to have a selection of logos with the edges antialiased with a veriety of colors and have the skin uploader choose which one they would like to use. Of course, this feature hasn't been implemented yet so you're stuck with what's there for now.
Phade.