Comment 2 for bug 549552

The transparency is being set by the theme (I assume you are using Ambiance or Radiance?)

Ideally, I'd like to be able to put a button in the preferences for gnome-terminal to select whether to use the theme for the background settings or not. Unfortunately we are passed UI freeze though so I can't really do this, so as a compromise, selecting "Solid" also tells the terminal to inherit the theme settings.

Only the Ambiance and Radiance themes are using this feature though, and it's still possible to manually control the transparency (and even set it to fully opaque if you like)