FFA's react with alkali catalyst and form soaps and water, during transesterification process. 

FFA is a high molecular weight compound, most likely affecting your viscosity and formation of deposits within the injection system and the engine, and to a small extent, at cold temperatures and low loads, your combustion. Not much immediate effect on maximum power, combustion and emissions.

Thanks Kamil Duda and Michal Vojtisek-Lom.