I think it's "something else", probably the name and the categories set for your desktop file; you probably have an additional entry for the Terminal somewhere in the menu now which does what you want and two or three generated from the old desktop file which don't. The name-field inside the desktop-file gives the applications an identity and the categories define the app's place in the menu. The .desktop-file that's installed by XUbuntu is /usr/share/applications/exo-terminal-emulator.desktop and has an Exec-line "exo-open --launch TerminalEmulator". I just right-clicked on the item in the menu and selected "Edit Application" (well, actually it said "Anwendung bearbeiten"; my system is set up in German ...) and got a small dialog in which I changed the command by just adding the option. That resulted in a new .desktop file which overruled the default one being written to ~/.local/share/applications with the change I made.
Holger
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