Try a resolution that's as close to it as possible, or maybe even a bit bigger. As long as your mouse pointer can't escape the game area, this should help. By the way, why don't you just run the game in windowed mode instead of a fullscreen mode inside a virtual desktop? It has the same effect, except now the game expects that your mouse can exit the screen so it may behave differently. Alt+Enter will put any Valve game in windowed mode, and it's an option in the graphics settings...
