It almost sounds as if, after awhile, his patella is causing some discomfort.
Did you discuss with your vet the problems his condition may cause in the future, such as pain?
Are his gaits off? (Look like he is limping?)
Another sign is increased "bobbing" of his head, and shortness of stride on his injured side.
If not, he may just be one of those lazier horses you really have to motivate to get out, or he may be getting bored.
Young horses have the attention span of about a four year old kid, so keeping lessions short (15 minutes) is good for them, but you can do 2-3 lessons per day.