I do not know how many people I have seen with this painting problem. It has taken me ages to find
the actuat cause but now I know. My HDD crashed 2 days ago so did a complete system restore. So when I came to do this paint and the windows looked like this I thought WTF????
But then I thought a bit harder and it came to me....... The only difference was that I had created my D92_tr_BS.TGA in........ PHOTOSHOP!
I had not installed paint.net yet. So I quickly downloaded paint.net and recreated my D92_tr_BS.TGA file. and as you can see my windows returned. So I looked a bit more into it and it turns out that:
Photoshop can not save a transparent tga file. It gives it a solid white background!
Paint.net however gives it a transparent background. SO basically DO NOT USE PHOTOSHOP to create the TGA file