On my Macbook Pro, apparently since 10.6.5, Guild Wars recently refuses to go "truly" full screen: 1280x800 is listed, but selecting it works very briefly, before falling back to 1280x778 (sic), with the Mac menubar shown above the game "fullscreened" window rendered in the remainder space.
To fix that, go into winecfg and disable 'allow window manager' and 'allow decorations'.