ECU rebuild/starter replacement

I have a1993 LS 400 with 200,000 miles on it. The starter went out and I had it replaced at considerable cost as it is almost impossible to get to. Car seem to run fine until the ECU went out 2000 miles later. Pulled ECU and shipped it to ATE for rebuild. Installed ECU and car started right up and seemed to run fine until my wife told me the passing gear does stange things. I found that at 4500 rpm the car would buck and jump. Checked for codes and none were found. My mechanic say that there is a Rev limiter in all cars to prevent someone from putting a car in Park, Neutral, or Reverse and over revving the engine. It seems that is what is happening with my car in all gears at 4500 rpm. Talked to ATE and they had me pull the ECU and sent it back to them. They said they fixed the problem and I installed it again and guess what??? Same problem. Do you think my problem occured with the starter rebuild or is it a problem still with the ECU? Car runs fine if you don't hit 4500 RPM.