Well... there are a few reasons for their 'falling out' around Wing Commander 3. The foremost of which is the fact that Blair had replaced Maniac as Wing Commander of the Victory -- when the previous Colonel, Dulbrunin, was killed in action, Maniac took over teporarily... he'd hoped to win the permanent assignment, but was replaced by his old friend/competitor.
Stresses were generally very high around that time, too, since it seemed to everyone that Confed was losing the war... Blair certainly wasn't happy to be assigned to the Victory, and Maniac wasn't happy to see him.