I've had this issue before and forgot how to clear it. I use the Win key a lot in key bindings. The issue now is that if a terminal is open and has focus, it will output some ASCII characters whenever I use the Win key - like starting medit with the Ctrl-W-l binding. Everything still works, I just have to clear the characters before using the terminal again. Minor annoyance.
The screenshot - note that the combinations Win, Ctrl-Win, Alt-Win cause different terminal output.
(http://en.zimagez.com/miniature/ascii-term.png) (http://en.zimagez.com/zimage/ascii-term.php)
As I recall, this is a simple fix done with reconfiguring the keyboard, but it alludes me at the moment.
Edit - Solved. Conflicting entry in $HOME/.Xmodmap file