We know Jellico did his homework and in fact read Riker's file prior to taking command. In my own personal canon, Jellico knew this guy might be an obstacle, what with his history of questioning orders (DeSoto, etc), and told him to change the shift rotation to see if Riker would do it.
When he failed, Jellico read him the riot act in Ten Forward and from then on, the person we see accompanying Jellico throughout the ship getting the departments in line is Data. Jellico was done with Riker the minute he failed to execute the captain's first order. I can't really blame Jellico. He was there to get stuff done and didn't have time for that BS. They were at the brink of war.