Sounds like you have BSP troubles. Your model might not be a solid. Look for missing faces. That´s the same problem i had with a carrier i made. The BSP problems made the hull full of "holes", where you could fly and shoot through.
Intersecting the mesh didn´t help me. You might need to manually check every face, looking for trouble spots.
I know i had to dump my model, because the problem couldn´t be fixed.
If i had to guess, i would venture the gun mounts as your trouble spot. Do an intersect, followed by triangulization, and try it. And even if PCS converts it, you might still not be out of the woods yet. You might need to check the model for solidity in-game.