Had the same problem with gtk3/compton/i3. Using i3 4.8-3, gtk3 3.14.9-1, compton v0.1_beta2-5 on Arch. The other fixes suggested here didn't work for me.
The following fixed the problem for me:
You need to edit the file ~/.config/gtk-3.0/gtk.css
.window-frame, .window-frame:backdrop {
box-shadow: 0 0 0 black;
border-style: none;
margin: 0;
border-radius: 0;
}
.titlebar {
border-radius: 0;
}
link: chjj/compton#189 (comment)
see also: numixproject/numix-gtk-theme#206