The semi-transparent problem (at the edges of the SKIN where it meets the map) is a SKINbedder problem. The picture of my car with a white box around it is a GooPs problem that is not present in nemaGE.
Good news! All the buttons on the right side of the skin work now!
. I will be releasing a new SKINbedder .exe with a more-working GE skin soon. It will probably still be another month or so before I have SbV3 final done (which will fix the semi-transparent problem by using layered windows for all the skin graphics).