Your entire X session should be a child of a login shell (that is, .bash_profile should be run by gdm when you first log in). It's only one login session for the whole X session, not one per terminal opened.
If your whole session isn't a login session then there's some other problem, but not a gnome-terminal problem.
Maybe it's due to the fact that gdm in the latest update is not working properly, and starts a failsafe session. Maybe it works with a new update.