Not sure about 2.5+, but here's how I would do it in 2.49:
First, make sure your ship is properly centered - there should be a ' Center New' button somewhere (in object mode), do this on detail0. Then, center all other LODs and the shield mesh to the same point (Shift-S -> Cursor To Selection to move the cursor to the detail0 center, then the 'Center cursor' button for all other lods and shield). Then move everything back to (0,0,0) coordinates; this is important, as PCS2 will assume your ship is centered there. Pressing 'N' should pop up a box where you can see any transformations applied to an object: the centerpoint location, and any scaling or rotation (if any scaling is not 1, or any rotation not 0, press Ctrl-A to apply it to the mesh itself).
If that doesn't do it, you may want to post the .blend file here, so we can take a closer look at it.