When you tested the 12.0 set up did you have a stock set up? Is the new set-up better breathing (less cats, larger diameter, etc.)?

Unless you are pulling AFR from right past the headers you are basically just seeing a compensation of more air being entered into the mix POST-Engine. That has zero effect on performance or engine behavior.

If you took an AFR reading from the tail pipe and one from the stock 02 location, the tail pipe would be about 0.5 pts different as there are additional obstructions.

For the most part nothing short of long tube headers will have any substantial effect on AFR.