Setting the lean protection lower won't do anything to the rest of the tune. Your tuner should know better than that...

The lean protection has two parameters (if I remember right), MAP and A/F. The lower you set the A/F number, the richer it has to run or it will hit the lean cut. When you dropped it to 12:1 you specified it has to run stupid rich, or the ECU will cut fuel (and therefore power) in an attempt to protect the engine..