Harmonic distortion is the addition of unwanted harmonics by your equipment. You have a high quality sub, and your aren't pushing it to it's limits. Harmonic distortion is probably not your issue.
The other harmonics are what cause a G on a guitar to sound different from a G on a violin. In other words, the harmonics are what give the instruments their individual "voices".
Your house also has a resonant frequency (as all structures do) that it will vibrate at when energy is applied to it, just like a tuning fork. Harmonics are also produced by that sound energy.
Any sound energy released will cause harmonics. Radio waves do it too. I believe that a vacuum is the only place where they do not occur.
John is probably correct here. The human brain is a wonderful thing. It takes data from multiple inputs, and makes it's own determinations. Maybe you brain hears the sound coming from the sub and can't localize it, but it can tell that the left side of your body is getting hit with SPL in time with the sound. It's just putting 2 and 2 together and getting the private school answer...
