EDIT: I should have mentioned that I’m running Ubuntu 10.10 Maverick 64bit on a laptop. I assume that other distros have the same issue, though.
Although ATM the launcher in the menu doesn’t actually do anything, I got around that by going to Ubuntu’s Main Menu preferences, selecting the Scrivener icon from the Office catagory, then clicking on Properties, and changing the launcher type from “Application” to “Application in Terminal.” Still launches a terminal window when Scrivener fires up, and if you close the terminal, of course Scrivener quits, too, but that’s not so bad.