In a case where any corporation, paying taxes in advance under the provisions of this act, shall pay an amount for any tax period in excess of the amount thereafter found to be legally due after the deduction of the discount allowed by this act, the Department of Revenue, or the Board of Finance and Revenue, as the case may be, shall establish a credit for such overpayment to the account of the corporation and issue to the corporation a certificate thereof which may be applied against any account due or to become due the Commonwealth.