You have isolated it to a mechanical problem by changing the ECU rom but more so seeing it with stock configuration.
This may be the problem
Check the fuel correction factor. (normally thrown off by poor CAI, leak in the intake system or problem O2 .)
Reasoning:
When the ECU is forced to make fuel correction (up to 25%) it throws off its ability to make adjustments when you go through the c/o loop transition. Because the AF correction is so far off the ECU cannot keep up with that transition.
Hobbes