Sounds like you've botched your profile up slightly by adding a custom command (something that runs as soon as it opens).
Thankfully you can edit your profile settings by running this (use Alt+F2):
gconf-editor /apps/gnome-terminal/profiles/Default
If you've botched up too much you can use the Etch-a-Sketch method and reset everything back to defaults:
gconftool --recursive-unset /apps/gnome-terminal/
Preface: I am new, and having similar problems. In the absence of an answer by someone with a functional knowledge of these things, this is how I am approaching solving this.
'man gnome-terminal' offers some interesting options for starting new windows, or tabs using a specific profile. An alias to start an instance of gnome-terminal in a new tab using profile "X" seems like a reasonable quasi-kluge, and allows for existing keyboard shortcuts to switch between, and close tabs.
It would look something close to this:
alias gtvim='gnome-terminal --tab-with-profile=X -t Vim -x vim >&1'
gtvim filename
For alias permanency, it has to be added to bottom of ~/.bashrc
I need to work on other things now, but that was my first foray into it. It still seems to open the command in a new terminal window, but still easily accessible from keyboard shortcuts.
Just as a side note, I am attempting to have all terminals with ssh connections to remote terminals open with a different color profile to help prevent commands being issued to the wrong machine.
Best Answer
In Gnome Terminal, click "File" → "New Profile"
For more details, see Gnome Terminal help - Manage profiles