This is how it looks with me:
Maybe another script is messing with it. How about this here... Find the line that says:
class Window_Sure < Window_Command
Just below should be this piece of code:
def initialize(width, commands)
# add another command, serves as fix
commands.push('')
super
@item_max, self.index = commands.size - 1, 0
self.x, self.y, self.z = 320-self.width/2, 240-self.height/2, 10000
refresh
end
Add this line before "refresh":