When you select something, the color of the selection usually changes to the font color, and the font color is being set to backgroud color. So, if you have a black background in a terminal, and the font is orange, you will get an orange selection and a black font color.
What would happen if you had a transparent window, and the transparency was set to 100%? Just take a look at the following pics.
The one with a black background:
And the transparent one:
Is there a way to change the font/background color of transparent windows?