I know exactly what the problem here is and it's not PCS2. Your pivots are centered by world corridors not offsets so even though it looks correct in the modeling program it's flipped when exported. Set your ship to top view. Mark down the world coordinates of the pivot. Center the pivot to 0,0,0 by typing in the world coordinates. Now move it using offset back to the correct position. Reset x-form and re-export. It should now be correct in PCS2.
I've seen this one so many times it isn't even funny anymore. The alternate method is to center the subobjects to 0,0,0 before export and them mover them back to the correct location in PCS2. If you are using something like truespace you will need to keep moving the center and object until they are both at 0,0,0 Sometimes it's a pain because you move one the other goes half the distance the other direction.
The above methods I've done both in MAX and the second one in TS7.6 with success.