I have not done any adjudication process for stamp DUTY but the stamp act says that :
1. Where stamp duty is not paid accordance with Stamp Act, an application seeking adjudication of revenue commissioner / authorised state authorities is to be made.
2. revenue authority will consider the application and order for payment of penalty as per prevailing state stamp Act.
3. If you concern iss on payment of stamp duty on share certificate, I suggest that you may issue the shre certificate in any other state and you can now bring the share certificate to your state and pay for differential duty. In case you need clarification you may send a mail or call me.
reg
Gopalrathnam M
9886618696