Ok I'm pretty sure the mission is called Trapped. You get trapped in an artificial wormhole and hunted by the Hirogen. Once your in the wormhole space the FPS drops horribly.
For one thing, I think you guys at Cryptic already know that your engine doesn't work as well in a large open space environment. Especially one that needs a lot of effects and a very high res skybox. I think thats why space zones are 1 planet + moons instead of a whole solar system.
Anyways I think part of the problem is that theres a lot of modeled space that the player never sees. I tried to take a screenshot of the map but it was all corrupted so I made a quick map.
Basically all the area on the right side of the map is unussed. I guess they were going to make the mission longer but probably cut it back at some point. I don't know how good your engine is at occluding polygons, textures and effects but I'm guessing this unused area is part of the problem. I also think the ammount of effects in this zone is hurting things as well.
2. My system should be able to handle it and hasn't had a FPS problem in any other part of the game.
Ok, as long as you got through it. So yeah, there is the Bajoran wormhole quest later, which uses the same map, and that "useless" space you mocked up. Thats prolly what it is, they used the same map for both quests, which I will even admit, is pretty bad
Its REALLY common to reuse assets in games. Although they go to far in this game due to the short ammount of development time.
One of the most obvious examples I've seen recently was the War Games ground portion when you've beamed onto the other ship. There is 1 hallway with a bend that has a hole into space that has a forcefield over it. They use that same hallway 3 or 4 times I think. Its only this noticable because of the same hole in the corner every time.