Assuming that the flat in question is situated in Mumbai and forms a part of a co-operative housing society governed by the provisions of the Maharashtra Co-operative Societies Act, 1960.
From a legal perspective, there is no difference in effecting a transfer of a flat in a co-operative housing society either by a mere transfer of shares issued by such a co-operative housing society by executing a transfer form or by executing a deed whereby both the shares and the right, title and interest in the flat are transferred. While the society cannot object to either of them, most people prefer the latter so as to document certain rights and other understanding between the transferor and the transferee.
From the stamp duty perspective, the Supreme Court has held that a transfer/sale of shares issued by a co-operative housing society would attract the same stamp duty as leviable on a conveyance. Therefore, the same amount of stamp duty would be payable on a transfer form whereby shares issued by a co-operative housing society are being transferred and on a deed of transfer/gift deed. Also, both instruments would have to be registered under the provisions of the Indian Registration Act, 1908, and applicable registration charges will apply.
As per the provisions of article 25 of schedule I of the Maharashtra Stamp Act, 1958, the stamp duty payable on a transfer form whereby shares issued by a co-operative housing society are being transferred or on a deed of transfer/sale deed, will be 5% of the market value.
If you have transferred your property to your mother by a gift deed, then it should have been done by executing a registered gift deed alone and not orally or by an unregistered document.