Originally Posted by SonicVQ

If a smaller fuel injector is entered into ECUTek (or any aftermarket tune/setup), the calculated injector pulse width (aka duty cycle) will be increased.

Then the ECM will look at the Air/Fuel sensor to determine how accurate the calculation as it compares calculated (or target AFR) vs actual.. If it is lean, more fuel will be added, and the pulse width (aka duty cycle) will increase.

With the above in mind, the duty cycle is the duty cycle.

When using ethanol, more fuel is required for the same amount of air.

For example, when using E50, the chemically ideal (stoichiometric) requires 11.9 pounds of air for every pound of fuel, or an AFR of 11.9:1. For max power it is 10.2:1.
In the example of E85, stoichiometric is 9.7:1, and about 7-8:1 for max power.

Pump gas stoichiometric is 14.7:1, and about 12.5:1 for max power.

If the proper injector size is specified in EcuTek and your duty cycles are in the high 90s, I suspect you need to increase the flow rate of the fuel pump.

How does your ECM know the ethanol content?