Igr issue in registration - can registration will cancel

Dear Sir I have got a house loan from a bank and registered a property by calling commision . The property was already running on loan from the same bank . So , there is case of book adjustment also from the bank on the seller account . I have paid the registration charges and stamp duty . The TDS is also paid . My contribution of 20 % by demand draft is also paid by me . I have also paid the 3.09% service tax to developer , as the seller has not registered the property before . I also have a possesion certificate from a developer . The registration was done by calling commision and bank has given a xerox of check to seller and asked him after getting the IGR from registered office , to take the physical delivery of check . Deed mentions about a book adjustment value , check number and my contribution draft details . Now , today when the seller went to Registration office for IGR , it was not provided as the registration office told him that , the extra 1.1% of stamp duty have to be paid as the property was not registered before and then only IGR will be provided . The seller and bank is asking me to pay this amount otherwise registration will get cancel , as book adjustment will change. Kindly advice , is it possible that registration to get cancel and my money getting stuck by no fault of mine . They are forcing me for 1.1% but I dont want to pay . I need urgent advice . PLZZZZZ