The overlay templates are all html if you changed something then it should work for all thumbs as your not changing the thumb but the overlay html
It sounds to me like maybe you need to actually change the overlay graphic? Since the image is actually the background changing the image background does not do much except when an image is not big enough to fill the background.
http://www.reeftalk.com/gallery/images/overlay-jag.gif
I hope this clarifies how this works. Your probally seeing the actual overlay image and thinking that would change color.