I do not think it's a smplayer / mplayer issue but rather a chrome - OS one, is it by any chance v11 ?
I did see a similar video-related issue on a friend's pc with chrome when after using chrome for a while with youtube vids and other normal websites, when closing or minimizing chrome the Win Desktop stayed "painted-over" with chrome's window.
IIRC since v10 they use video hardware acceleration (webGL) which is also used by mplayer vo so they maybe conflict.
Firefox 4 uses it too but not forced.
Could you try to see if this also happens if you disable it:
http://blog.laptopmag.com/enable-hardwa ... -firefox-4Cheers.