Paymentof extra stamp duty

Dear all, We are Maharashtra based 100% subsidiary of Japanese Co., recently we have issued some shares to our parent co. While paying stamp duty on share certificate I have paid same through ESBTR challan , however , for one of the share certificate stamp duty is less than Rs. 5000 only Rs1200. I could not create challan for this. I understand that this share certificate will required to be franked instead of the ESBTR. All other share-certificate has ESBTR challan and only this single sharecertificate will have stamp on its face. My management has suggested may to pay Rs. 5000 stamp duty for this share certificate as well and get similar challan for this share certificate too. Now , my query is whether same shall be questioned by the stamp office if I pay Rs. 5K instead of Rs.1.2K. Will it be treated as violation of stamp act if I pay extra stamp duty on share certificate.