Profession tax is not a tax on "salary" but it is on any income received and, therefore, stipend will attract profession tax. Now regarding receipt, it is not the employer who will issue the receipt but the Local administration, ie, Kochi Corporation, who will issue the receipt. It may also happen that the Corporation may issue one receipt for the entire amount paid by the employer on account of employees and in such cases individual receipts may not be available. You can also see that in your Income Tax form 16 issued by the employer the amount you have paid towards profession tax, Rs 2500 (1250 for half year) will be shown as deduction from the salary income. This will support your stand of having paid the profession tax.
Madhu.T.K