If he can go in 59 to a jog cart he seems to have some ability. Is he good gaited? Does he hit a knee?
Does he jog and train by himself or with other horses?
It may just be he gets too wound up behind the gate. You might try ear cones to keep him calmer. http://www.bigdweb.com/Ear-Hoods/products/390/
If it's an issue with the gate, if you have access to a leader hook him to that for 5 miles a day (around 17 MPH) and he'll get used to following the gate. Then sit behind him behind the gate and have the leader like the start of a race. They generally get it pretty quickly.
How many lifetime starts? It takes some horses a while before the light bulb goes on and they figure it all out.
Good luck with him.