He was accused of abusing his post by preventing or delaying the return to their owners of fugitive slaves that had taken refuge with the Indians.
[4] Humphreys took up his position as Indian agent in Pensacola in late December 1822, but did not receive instructions on his duties until the next month.
[5] In the summer of 1823, Humphreys conducted about 350 members of Indian bands that lived west of the Suwannee River, including the Miccosukees, Tallahassees, and Apalachicola band, almost 300 miles (480 km) from St. Marks to the conference site 5 miles (8.0 km) south of St. Augustine where the Treaty of Moultrie Creek was negotiated.
Then, in July 1824, as Duval was personally confronting Neamathla over the move, Humphreys left Florida without notifying the governor he was taking leave.
A detachment of soldiers from Fort Marion, accompanied by White civilians, found the Seminoles at Cabbage Swamp, north of St. Augustine.
Starving Seminoles left or turned back from moving to the reservation, and killed cattle belonging to White settlers.
[11] In May 1826, Humphreys accompanied seven Seminole leaders, including Neamathla of the Apalachicola band, Tuckose Emathla (called "John Hicks" by English speakers) of the Miccosukees, Micanopy, chief of the Alachua Seminoles, Holata Micco, of the Peace River band, Tulce Emathla, and Fuche Luste Hadjo, also of the Alachua Seminoles, to Washington, D.C. to meet with James Barbour, United States Secretary of War.
When it looked like violence might result from the rivalry of the factions, Humphreys requested troops be sent from Cantonment Brooke (on Tampa Bay) to help maintain peace.
The Army at first proposed a temporary post on the Suwannee River, but Humphreys and others protested that place was too far from the reservation.
As a result, the new post, which became Fort King, was placed 0.25 miles (0.40 km) from Humphreys' Indian agency.
[14] Humphreys tried to defend the Seminoles against White settlers so strongly that a grand jury presented an indictment against him in 1827.
[15] Ownership of Black slaves was a major disruptive issue between White Americans and the Seminoles of Florida for most of the first half of the 19th century.
The issue was important in the attempt to seize East Florida from Spain in 1812 and the First Seminole War of the late 1810s.
[17] Legal procedures for handling disputes between Whites and Indians over ownership of slaves had been established, but failed to ease the problem.
[18] Humphreys was charged with obstructing the return of runaway slaves in hopes that the loss of time and money would dissuade the owners from pursuing their claims.
Despite orders about not doing business with the Indians for whom he was appointed agent, Humphreys was involved in the slave trade with the Seminoles.
Andrew Jackson was elected president of the United States that year, and Duval asked him to remove Humphreys and the judge who had ruled against withholding the annuity.
Fort Defiance was abandoned later that month, leaving all of Florida south of Newnansville and Black Creek and west of the St. Johns River to the Indians.