Well I finally Broke mine in today and I had a similar problem as you. What I noticed is my Transmitter was actually shutting off/on. I Don't know if your having the same problem... What I Finally figured out though was the some of the - Battery tabs in the transmitter were not making a good contact. So I took a flathead and bent them out a bit, re-installed the batteries and so far so good. I ran it for about another hour with no problems. I hope that helps.
Side note: this is the third engine I have broken in and I must say it is by far the easiest! I had it broken in and tuned perfectly by the 5th tank. Engine runs right at 205-215 with plenty of power. Only problem I have is my wheels wobble... Everything is tight and straight. Anyone else have this problem?? Overall though it's a great little truck.