this sounds like the same problem I had way back when I was playing the game. it was long before the end of the game. If you don't go to www.lucasarts.com
and download and install the patch for the game, you will play the last level too soon and it has the problem that you describe. You need to get and install the patch and then start from your last savegame near the end of the previous level....then when the next level starts, it will be the new version. Other than trying to use that savegame, don't use any of your old savegames after installing the patch....and don't start with any of the level starts either. Name your new savegames differently so you can tell them apart....or delete the old savegames.....or start the whole game from the beginning.