alright, as a test go to ATO->Body, Text & Links->Body Style and change the line
HTML Code:
background: #ffffff;
to
HTML Code:
background: #00ffff;
and take a look at the site. Any change?
If you are talking about the color picker, say at ATO->Body, Text & Links->Link Default Color, there are two parts, the color picker (the left side) and the intensity (the right side), If you don't move the intensity slider up, the result will always be black.