Yeah, sorry about that. I'll update the first post with how to fix this. You see, Advance map overwrites the values with 'FFFF'. Which is why most level scripts won't work if you do it through advance map. I'll update the first post with how to make a level script through XSE, or for those who don't like XSE, through hex. The only thing you'll need from A-map is the 'Professional Header' and the 'Map script offset' from it.
You will eventually need XSE to check the script though...And Advance Map with a Hex editor.
Get prepared everyone!