Your case is slightly complicated now. You are saying that the previuos owner paid stamp duty but did not register it. It may be that he may not have paid adequate stamp duty and that was the reason that he did not register it. Has he handed over to you his conveyance deed? You can find out from the registrar's office what was the ready reckoner value of the flat on the date of purchase of the previous owner and whether it matches with the value mentioned in the document and the corresponding stamp duty? From whom did he purchase the flat? Was it from the builder or from previous owner? If from previous owner is there the conveyance deed under which the previous owner purchased? If the seller has handed over to you (he should have) his purchase deed, you can take it to the registration office and try to get it registered. You will have to make up for the inadequate stamp duty paid and also pay a heavy penalty. Actually your seller is liable to pay because it was his fault. But the registrar "may' accept if you offer to pay. Alternatively you can ask the seller to pay.
The Society was right in not handing over the share certificate to your seller. Now the seller has taken you for a ride. If you file a suit now against the seller for the share certificate, it will be a long drawn process. Instead you pay the stamp duty and penalty and get the share certificate from the Society . You file a suit against the seller to recover the amount which you paid. You take the Society into confidence before doing all these, so that they do not give you further problem.