I have an XML file for a custom profile for gnome-terminal. However, when I throw the file into an appropriate directory like ~/.gconf/apps/gnome-terminal/profiles/Default/%gconf.xml the file is clobbered the next time I run gnome-terminal. The problem happens also if I make a new profile and manually copy my xml file over the newly created profile's xml. It also happens if I perform the copy actions when gnome-terminal is not running (I log into one of the psuedo-consoles and thus can't be running gnome-terminal). No matter what happens, the next time I run gnome-terminal, the profile colors aren't applied, and the %gconf.xml file that I had edited is changed to the contents of the default profile (as I said, clobbered).
I'm running ubuntu 10.04 with the gnome desktop.