Loring famously butted heads with superior officers, particularly with Stonewall Jackson. At the conclusion of the Romney Expedition in northwestern Virginia (now West Virginia) in January 1862, Jackson returned to his headquarters in Winchester while assigning Loring to stay and occupy the small, mountainous town. Unhappy with their assignment of holding a remote outpost in the dead of winter, Loring and his officers went over Jackson's head to Secretary of War Judah P. Benjamin, requesting that the division be withdrawn. Jackson complied with the order, then resigned in protest of Richmond's interference with his command; he withdrew his resignation under pressure from Governor John Letcher and his former commander, Joseph E. Johnston, and Loring was reassigned out of Jackson's command, and given command of the Department of Southwestern Virginia. In his five months in that role, Loring moved a force of 5,000 into the Kanawha Valley, ultimately occupying Charleston for a six-week period. In mid-October, Loring was transferred to the West.