I just upgraded to Ubuntu 14.04 and I have the same problem I've always had after an installation/upgrade: the terminal's transparent background shows the desktop (not the window that is behind it). I've seen this question.
Most of the time,
gconftool-2 -s '/apps/metacity/general/compositing_manager' --type bool true
will get it to work, but this is not the case anymore. I've also tried compiz --replace which does work, but then screws a lot of other stuff up and makes things pretty unusable.
Is there anything else I can do to
$ gnome-terminal --version
GNOME Terminal 3.6.2
Run this command:
And then adjust the transparency settings in the profile preferences.