How big is this thing?
If it's ... gigantic... you simply may not be able to see it,because all of the polys are outside the camera viewing area.
Other possible causes:
1. Yes, there's an art to resizing things. FLModel tool makes it pretty easy, but it still requires some practice. It's possible (not probable, but possible) that the ship's not sized right.
2. If the ship's waaaay off the centerpoint, that's a possible cause, but I doubt that's happening.
3. The SUR needs to be the same size as the ship, in terms of its outer bounds.
4. Mixing TGA and DDS textures on a single CMP has had this effect. Check out the MAT file with UTF Edit, and export the textures (you'll need to add the file extensions by hand... MIP0s are TGA and MIPS are DDS... and DDS textures require a special plugin, which you can download from nVidia).
I should admit (sheepishly) that I've had similar problems with ships that look great in-game... that will show up in Equipment Rooms and the Shipyards... but won't show up correctly during landing sequences. I'm hoping that the next version of FLModel Tool resolves these issues for me
Hopefully somebody with more hard-core experience has some other things to try (hey, maybe I can resolve this for my ships too, hehe).