Well the threshold for stamp duty is now 125,001 (upto this price you dont pay any as it changed recently). The Vendors solicitor will have some sort of paperwork saying the purchase price as will the estate agents.So the inland revenue cannot soley rely on the TR1
On a form you would have received from the agents called the memorandum of sale it says the purchase price and the Vendors solicitors - maybe you should give the solictors a ring to find out why the paperwork is wrong as its the solicitors who should be forking out the cost if the inland revenue will not waver the charge. If you dont have a copy you are within your ask for another one form the estate agent - hope this helps a bit! good luck