According to this site: https://www.auran.com/planetauran/dls_cleanup_list.php
the asset was repaired and uploaded by a third party. In that case it is difficult to know what the original creator intended for the windows, as the asset was not working in the original revision. It is possible that the required repairs included changes to the way that the window textures were specified (eg changing from BMP + transparency to ARGB TGA). If that's what has happened then they can end up with a different transparency. You can edit the window TGA files to adjust the transparency to your own requirements.