You say he's a good handling pilot... May I ask what his flight planning is like for an actual navigation trip? Does he, can he? Whats his airmanship and technical understanding like of Nav (and the other subjects)? What was he like for the exams he's already passed?
As Genghis has intimated...it may be just his learning style that is the problem...
If he can do the stuff in 'real life' in real time it may be just exam nerves.
External stressors?