Subwoofers are a strange beast.
It is very easy for a sub to set up a standing wave. If the wave is reflected it will cause peaks and troughs. I had the exact problem with my subs (JLAudio 113s).
You indicated that when you changed the phase 180 degrees, you got a peak.
Unfortunately, there is no easy answer.
I found that if I placed the subs on pedestals (8" high) and then repositioned the subs, I could minimize the reflections. Also trying using acoustic bass panels (like Cathedral panels) to help control reflections.
In addition, I set my subs as master and slave, so ARC thinks it is only one sub. (Remember that low bass is non directional; the human ear is not able to detect where the sound originates.)
ARC was able to correct the sub curve.
For fun, try this site to see the impact of reflected waves http://www.hunecke.de/en/calculators/loudspeakers.html