Thanks for the saved game Veki, that's exactly what I was looking for (terror mission on the map with Triton en route).
I let the Triton land, then immediately saved the game into a fresh slot. When I looked at the aquanauts in the mission though, they were not up to the task of testing so I went back and upped their stats and edited craft.dat to give them some MC Disruptors. Then I cleaned out the save slot, reloaded the game, waited for the Triton to land and saved again in a fresh slot. Much better.
Here's a pic of unitref.dat in MS-Edit:
It's a clean save as you can see, and yep, there is a naturally occurring Xarquid on the map. Take a gander at the terrorist listing though, it's pretty messed up. Since this happened in my game without using a loader and a clean save, I think it's safe to eliminate the loader or overwriting which causes these problems. My only guess right now is that the skill level (Superhuman) causes the messed up ordering and Xarquid substitution, because on Beginner I never saw this.
Oh, and by the way, there are
Triscenes on the map. Some of them are spawned in incorrect locations too leading to them being stuck and unable to move.
Will continue to research this as time permits. (Maybe this weekend). We'll get to the bottom of this yet folks!