Make sure your texture has "-trans" addon in filename. Some time ago code of transparent textures was reworked, and now to tell the engine which texture is transparent, you must include "-trans" in filename. For example, default cockpit glass texture in old MediaVPs was just "glass", and now it's "glass-trans". Unlike -glow, -normal or other additional texture channels, filenames with "-trans" works as diffuse map itself so "glass-trans" does not require just "glass" to work. This may be confusing.
If I remember correctly, you used to include glass texture in your combined textures which contans various details [confed_details_1 and 2]. Now if you include any transparent element with non-transparent ones like you did before, this glass won't be displayed correctly. If you add "-trans" to filename of such texture, rest of elements is also likely to appear transparent ingame.