Well, that's weird.
You should avoid putting mod data in folders where it's not designed to go. Use the FSO Installer or Knossos to make sure the mod is installed properly.
It sounds like the Deneb III transparency issue is a FSO bug though. What build are you using?
The problem is, too many mods folders for simple campaigns, destiny of peace, awakenings and deneb 3 should be all part of FSport if you ask me, destiny of peace is fine, awakenings causes a problem with the Asimov on FS port that im trying to figure out and fix, Deneb 3 is also fine from what i can tell, except the Lucifer is also using the planetary beams on the Aquilade Arcadia (easily fix).
You may dont agree with this, but i do that in order to remove unecessary mod folders.
Abou the scape pods i have it on video, but im petty sure is caused by some other unreleated error on FS2 3.8.0, it works after reloading FS2 (reloading mission does not work).