only the five files
GS_Asteroid.fx
GS_Planet.fx
GS_Ship.fx
GS_ShipBuilding.fx
GS_ShipPhasedOut.fx
from THE MOD's PipelineEffect folder should be removed as the ones in the main game folders ARE the correct ones AND are needed for sins to work.
have you tryed verifying your sins/entrenchment/diplomacy install?
harpo