In 1846 George James Armytage stated that he saw Rev. J. Duffus drinking and smoking in the tap room of a public bar. Broughton appointed a commission to investigate whether the charges made were legitimate and worth further investigation. After hearing from numerous witnesses who testified to Rev. Duffus' good character, the commission concluded that there was insufficient evidence to carry the investigation any further. In 1847 charges relating to Duffus' moral character were brought against him by the church wardens as a result of documents they had received from Mrs. Forbes and her daughter Mrs. C.A. Bull. Broughton again appointed a commission to investigate the validity of the charges.
The commission concluded that the charges were legitimate and should be investigated further. Broughton therefore held an ecclesiastical court hearing in which he heard the witnesses, and passed sentence