Since 11.10 you can't change much in the appearance options, just the windows border styles but NOT the background colour like you could do it in Natty.
For some odd reason as I upgraded to 11.10, it took the colour theme I had in 10.04 - a greenish background which suited pretty nicely to my wallpaper and my custom emerald theme.
Now I have a mix of those colors, it looks HORRIBLE.
I tried using
gnome-tweak-tool but you can't customize the window background color.
For those who have the same issue, I found a solution in this blog post
I just reset to default the