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I just downloaded it and took a look at the Dungeon in the editor. Honestly, I didn't see anything wrong, meaning everything looked clear. Either there's something wrong with the editor, or there's a glitch in the map itself. Just in case, it's best to double-check.
And regarding the transparency – perhaps you meant those texture duplications, where the terrain under an object is uneven. Usually, such errors are reported in a message before saving the map.
As far as I've checked and played the game, I've never encountered anything like that on this map; everything is normal. I don't even quite understand what the issue is? Is there an uneven surface under the objects somewhere? What does that mean? It's just the landscape... why would it be see-through? I might be able to fix it, but I need to understand what's wrong.