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Sorry I'm a little late to the party on this one. It would seem that engine loads could be the issue if you're hitting loads over the ones in the load limit tables.
What I will say is that in ECUtek the only tables that I can find that seem to differ between auto/manual:
Open Loop Throttle Thresholds. Auto has high/low altitude tables, manual only has one - these are both defined for both I and G which suggests different table locations.
Open Loop Per Gear RPM Thresholds
Ignition Timing Idle (In Gear) Above Threshold
There's nothing that should affect open loop fueling.
Have you also checked the open loop fueling additive? If you're hitting different loads then this could also be coming into play.
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