Make a variable. Check the box to show it. Drag the variable off the Stage into the palette, it goes away, but the variable remains checked for 'Show' (would make more sense if it unchecked when the variable is dragged off). Click the box to make the spurious check go away, actually it causes the variable to Show on the stage again. (Click one extra time to hide the variable)
Yes, that drives me crazy too. We know about it. Thanks for pinging it.