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So I'm almost done with the game and have completed the fox and geese puzzle but after I last commanded Isis (to pull the rope in the mine) the command box stayed on the screen. Now I can't click on any of my items so I can't finish the game. I'm really frustrated and don't want to have to play the whole game all over again. I also have looked everywhere for the answer. Please help. Thanks.
Have you been saving your game as you go along, and do you have a save game from just before you gave Isis the command to go through the tunnel to the rope? If you do, you can load the game from that point and just re-do from that point. I always recommend that you save your game often - even if you sit down and play it from start to finish without stopping - because you will always have a way to undo anything that goes wrong without starting at the beginning.
As for the command box sticking, I never had that problem. It always went away as soon as I turned away from Isis. If you don't have save games from before the command box got stuck, and if you saved the game before exiting to post this message, have you gone back to it to see if the command box has gone away when you start it up again?
I just noticed something that I passed over before - did you use the command box to get Isis to pull the rope? You only needed to use it to get her through the maze and up to the tunnel where the rope was hanging. To get her to pull the rope, you only needed to click on the pulley that the rope is hanging from and she automatically takes the rope and pulls it. I don't know if this is what caused your problem (using the command box when you didn't need to - if that's what you did), it might also be a glitch in your game.