In your first screenshot the transparency map is NOT the copor map but a specific transparency information. The color map has a sort of general gray level that is interpretated as transparent of course too. And makes the whole thing a little transparent. In this case i think there is a specific transparent bitmap somewhere, often has an extention of the name ".._a" or "..._trans"  You should look for that.

What else can be is that the transparency channel in the tif file that's used for the color map here is missing. Can you check those tif files in something like Photoshop?

One day your ship comes in - but you're at the airport.