Greg21, here's an explanation for that strange behavior. bash can start in two modes, a login shell and a non-login shell. When you login at the CLI, bash starts a login shell. Normally, when you start up a gnome terminal, bash starts a non-login shell.
In a login shell, bash looks at /etc/profile and the first of ~/.bash_profile, ~/.bash_login, and ~/.profile
In a non-login shell, bash looks at ~/.bashrc
That's why your gnome terminal prompt, colors, and other stuff looked different from what you normally get when you log in at the CLI.
As neenee has pointed out, you can set gnome terminal to start up as a login shell, which you have found acts just as described above.