The company stopped paying Pinkerton in late 1788, as the costs were exceeding the original estimates, and the contract was taken away from them in February 1789. There was then a financial dispute over money which had been paid to Pinkerton as "extras", but which the company then claimed were overpayments. Some £2,750 was at issue, and the case rumbled on for a decade, until a court case in 1801 gave him only £436 of the claim. Unhappy with the outcome, Pinkerton justified his position, but his remarks about John Houghton, the Company Clerk, were deemed to be libellous, for which he was fined and spent some time in prison.