Hi Vikas,
In case of STO the standard billing document(Proforma) JEX is available. For this billing document accounting entries will not be generated. with reference to this billing document you can created the excise invoice directly through T.Code J1IIN to create the excise liability.
Then coming to your query as Mr.Lakshmipathi mention kindly first be clear about the process & the issue that your are facing. There are lot of threads regarding STO process with excise invoice.
Why your are raising the excise invoice through J1IS?
As mentioned by you in the post why you are checking the accounting entries in VF03 in STO process?
A invoice has been created, during J1iin, excise entries posted not done.
I check the same in VF03.
The process flow for STO process is PO->Delivery Doc->Billing Doc-JEX(Proforma) No accounting entries->Excise Invoice(Excise accounting entries will be generated here)->Goods receipt in the receiving plant->Post excise invoice.
Hope you are clear now.
Regards,
S.Himavanth.