At Pisa Thomas worked very hard on his commission, sometimes 14 hours per day. The strain was too much for his wife, perhaps depressed also by her loss. She ran off with an Englishman, but later returned. The issue of adultery came up again. Violent accusations followed, indignantly repudiated; a diplomatic correspondence ensued, and a demand was made, and supported by the grand duke, for an apology, which the professor refused to make, preferring to lose his chair. He set out once more for Scotland, but was intercepted by the Florentine cardinal Luigi Capponi, who persuaded him to remain at Bologna as professor of Humanity. This was the most distinguished post in the most famous of continental universities, and Dempster was at the height of his fame. Though his "Roman Antiquities" and "Scotia ilustrior" had been placed on the "Index" pending correction, Pope Urban VIII made him a knight and gave him a pension.