I don't know the answer but have wondered the same thing. My assumption is that the engine was running out of RPMs sooner on just the primaries, and the optimal shift point is likely different between the two experiments.

Did you experiment with shift points? What were the incrementals on the 14.09 run? I wonder if the times show the car falling off on the top end. Did you have anyway to confirm the AFR was reasonable on just the primaries?

Look forward to seeing your results.