Question:
Is this with your subs plus mains or just the two subs?
At low frequencies, the plots without smoothing just don't get so jittery as the higher frequencies (you can see that in this chart as it is very smooth from 10 to 20Hz and starts to get crazy by the time it reaches 300)!
I'm betting if you took the speed of sound, calculated how long it would take sound to travel 3.1 feet, you would get a pretty good estimate of the duration of the miniDSP's ADC, internal processing time, and DAC!