Almost immediately after the Burke and Hare case, the Royal College of Surgeons of Edinburgh began to harry him, and by June 1831 they had procured his resignation as the Curator of the museum he had proposed and founded. In the same year he was obliged to resign his army commission to avoid further service in the Cape. This removed his last source of guaranteed income, but fortunately his classes were more popular than ever, with a record 504 students. His school moved to the grander premises of Old Surgeons' Hall in 1833 but his class declined after Edinburgh University made its own practical anatomy class compulsory in the mid-1830s. Knox continued to purchase cadavers for his dissection class from such shadowy figures as the 'Black Bull Man,' but after the 1832 Anatomy Act made bodies more available to all anatomists, he quarrelled with HM Inspector of Anatomy over the supply of bodies, and his competitive edge was lost. In 1837 Knox applied for the chair in pathology at Edinburgh University but his candidature was blocked by eleven existing professors, who preferred to abolish the post rather than appoint him. In 1842 he was unable to make payments to the Edinburgh funeratory system, from which bodies were supplied to private schools, and he relocated to Glasgow where, still short of subjects for dissection, he closed his school in 1844. In 1847 the Royal College of Surgeons of Edinburgh found him guilty of falsifying a student's certificate of attendance (a not uncommon practice in private schools) and refused to accept any further certificates from him, effectively banning him from teaching in Scotland. In the same year he was expelled from the Royal Society of Edinburgh and had his election retrospectively cancelled.