Comment 3 for bug 1260383

I have a similar experience as you, but for me it seems that it isn't caused by Pantheon Terminal, but Gala.
For me, transparency works in both gnome-terminal and pantheon-terminal when using Unity, but neither of them work as expected when using Gala. (This is with gala and pantheon-terminal from the daily ppa under Ubuntu 13.10, so it's not the same setup as yours).

Does e.g. gnome-terminal's transparency work with Gala for you? And does pantheon-terminal's transparency work with some other WM?