Stack height may have changed.

Stack height is the distance from the bottom of your foot to the center of the pedal spindle. Different pedals, thicker or thinner cleats and soles may have changed stack height significantly and this could account some of what the OP feels.

@Defyme, measure the stack height of each setup if you can. Adjust saddle height relative to the bottom of the pedal stroke accordingly.

Edit: beat me to it, but yeah.