Mace, welcome. You haven't described your room dimensions or the location of the sub, but if one dimension is about 16', then yes, there would be an axial mode due to that dimension at around 35Hz(i.e. 560/16). It's possible that the strong response around the peak in the 40Hz area gave the impression of stronger bass at the 180 setting. Your present readings are exceptionally good for in-room response. How could such a flattened response possibly "muddy" the sound? Flatter is better than louder.
