We've had similar issues on our setup (QX6.1/OSX10.3.3)and were especially prone to this when opening up really old docs (those created 5 or more years ago - around v3.3) which would assign themselves 'apple w' - not the best.
We tried quitting Quark, restarting the Mac, but eventually had to reboot our external HD on the network which holds all our files to remove the shortcut.