Tell us more about the auto setup feature. Does it match the sub level to the speaker level, or does it attempt to do some equalization or correction for acoustics?
If it does EQ then my feeling is the effect you describe should be minimized or eliminated but at one listening position only.
If it does not do EQ or acoustics correction then I would say the effect you describe is mostly due to room modes (standing waves) causing ripple in your sub's response.
I think to solve that:
Use an EQ or room correction unit, but it will really help at one position only. Units like Audissey (built into some HT receivers too) attempt to do multiple position correction, but IMHO this is still a compromise.
Use multiple subs to reduce the effect of room modes. Four subs can almost eliminate room modes and give you a very smooth bass response. Hard to get past the wife though, but two subs can give a meaningful improvement without alienating her...