When you changed ECU's did you use the same number ECU as what was in the car originally ?
Why I ask is because I have a T5 manual VS which now is running on a Auto ECU (VT I believe) The Kalmaker Software Tuner did the tune on the Chip & sorted it all out. Now the only problem I find is on a trailing throttle yhe revs will blink up & down, the same as you find with a Auto Trans Commies. So even though I have a memcal tuned for manual operation in the ECU, it still has some operating traits from the Auto ECU so it seems.
I wondered if your ECU went from a Auto to Manual possibly ?