You can change the window border transparency using the gconf-editor. You can change the window transparency for all the window borders or for active window borders. To change the window borders transperancy you need to have the gconf-editor installed.
To install the gconf-editor open a terminal window (press Ctrl+Alt+T) and copy+paste the following line:
sudo apt-get install gconf-editor
To start the gconf-editor press Alt+F2 and type: gconf-editor.
When the configuration editor is open click on apps -> gwd and change the value of the metacity_theme_active_opacity and the metacity_theme_opacity to a value lower then 1.0. To change a value all you have to do is double click on the name and change the value in the edit key window.
metacity_theme_active_opacity: changes transperancy for active window borders
metacity_theme_opacity: changes transperancy for all window borders