The special effects (Compiz) of ubuntu windows use the GTK by default. To adjust the transparency of the windows just go to the configuration editor of GNOME and change the values in the way you want. 
1. Press ALT+F2 to open "Run Application";
2. Write gconf-editor and run;
3. Go to apps->gwd and you’ll find the following lines:
metacity_theme_active_opacity -> Value of transparency of the windows on which we are working;
metacity_theme_opacity -> Value of transparency of the windows which are behind.
Value "1" indicates "without any transparency"; value "0" indicates "maximum transparency" (other than invisibility).
Adjust the transparency of window decorations