Hi Almeida,
We found that problem was due to wrong assignment of Item category and MRP type combination settings for determining shcedule line categories.
We maintained BP for quotation and CP for sales order. Because of which when we create sales order system was copying inquiry number to the production order due to which we were not able to see the sales order in the MD04 List.
Now when we changed the schedule line category of quotation from BP to BN system is passing on Sales order number in the MD04 list which is as per our requirement.
Thanks for your valuable reply. I have put above reason, so that if it can be helpful for others who face similar problems and if you want you can include that in the document shared by you.
Once again thanks for prompt replies.