When I set up my stereo pair of 2Wq's (with my Vandy 3A Sig's), I tried them both in-phase and reversed-phase, and the outcome was similar to what you describe. I subsequently got the Rives Audio test CD (which has test bands that are corrected to work with the Radio Shack SPL meter), and tested the subs' frequency response while making small placement adjustments (as Plato describes). After several hours of moving the subs a few inches nearer or further away from the side and rear walls, and driving the subs in-phase, I eventually got a much flatter frequency response. The Vandy subs, in my experience, take a good deal of experimenting to find the best placement, but then reward you with full, fairly flat response.
The frequency response of the Vandy 2Wq sub also depends on the "Q" setting that you choose. The maximum "Q" setting (lowest number on the dial) gives you the flattest response, while the higher settings have a pronounced "hump" in the frequency response. When adjusting your sub(s) your subs, I advise you to begin with them in-phase and the "Q" setting at its lowest number.