CVD gl hitting in grn and j1iex during Imports

Dear Experts,

I am facing different issue during imports, in a single SA/PO CVD  crediting and adding to material cost.

here is the process

1.SA/PO

2.Commercial invoice:

          Customs clearing GL dr

          CVD clearing        GL dr

            Commercial office   Cr

     (entry is correct)

3.GRN

      Stock GL  dr

     Gr/Ir  clearing cr   

     CVD clearing  cr

     Customs Clearing cr

     (means CVD adding to material cost which is not correct)

4.Excise invoice post:

     BED,AED dr

     CVD clearing cr

     (entry correct)

we have checked every thing but not getting it ,can some one help on it how system posting at both times.