Please make it as a single shipment if mulitple products are bought in same order and shipping charges should be charged only once where shipping charges are applicable.
Refer the attached file:
Shipping charges are applied multiple times instead of one.
But according to your reports now the bill amount & remittance is pending for the period of 01.04.2016 to till date. & which file i will share with you contains the courier charges before this period.