Vide Public Notice 09/2015-20 Dated: 16th May, 2016 it war clarified that

• The marking of tick in pursuance of the earlier Public Notice No.47, dated 8 th December 2015 i.e field tag of reward scheme in shipping bills if endorsed  as "YES" it shall be treated as declaration of intent in case of EDI shipping bills.

3.04 Entitlement under MEIS

Exports of notified goods/products with ITC[HS] code, to notified markets as listed in Appendix 3B, shall be rewarded under MEIS. Appendix 3B also lists the rate(s) of rewards on various notified products [ITC (HS) code wise].

The basis of calculation of reward would be on realised FOB value of exports in free foreign exchange, or on FOB value of exports as given in the Shipping Bills in free foreign exchange, whichever is less, unless otherwise specified.

The shipping bill FOB value are inclusive of commissioner up to 12.5% , therefore the MEIS duty credit is available with inclusive of commission up to 12.5 percent whereas the ecom module is reduce to duty credit even if the commission are beleow 12.5%.

Thus the ecom validation needs to be rectified appropriately.