Ugh, Luddies legacy.
Short of reposting my post from that thread again let me sum up...
It does work fine but I tweaked it and renamed things cause he (Luddie)did a straight rip from SFC3 and didn't think.
Neo- are you sure it is in game? I mean do you see an invisible ship fire? When I started modding FS2 my first insert was the Xanthus. I couldn't see it except for a wireframe and was like that, it worked in game but since the textures were not available it WAS invisible and it could attack others but not be hit (weapons fire would go through it ineffectively).
Once I renamed the textures to stock FS2 ones the ship showed up and then I used them as a base and retextured it to my liking (problem solved).
Also you indicated you are using core FS2 directory files, a big no no until you know what you are doing. make a MOD folder of any name (I made mine FS2SFA for Starfleet Academy I also had folders for Gundam, Robotech, and my other projects before they got lost) and use the data folder you make in there!

Before I ran into IP issues cause of Luddie I reconverted most of his "work" for my mod since his "Read Me's" gave blanket permission to all (of OTHER people's work) and all the ones I did worked.
Did you do any tweakage of Texture names and forgot to make them match what the pof actually has listed? I've done that before and didn't notice cause I had both sets in the same folder and if they are similar it can slip by you easily.
Note - you should NOT be seeing a wireframe or mesh texture of a ULY!! Or if you see one in the mission itself! This means FRED cannot find the right pof to match your table and it uses the ULY be DEFUALT!
IIRC - as I haven't modded in 5+ months