In full screen mode the "clickable" area of everything is moved down 50%, so the top half of anything that can be clicked on either does nothing (in the case of menu buttons) or ends up causing you to click on something else (in the case of dungeon tiles).
Tested in Internet Explorer and Firefox 4. In the meantime I'm using CTRL+mousewheel to zoom in but full screen is definitely the preferable option.
Win XP Pro, SP3
GeForce 9400 GT