Stay standing while listening in 2ch.
Fred covered why this is happening in an earlier post
"Nulls can happen in any of the three directions in your room."
Nulls are created by the dimensions of the room and the frequency that corresponds to these dimensions are either enhanced or cancelled.
With the subs on you are feeling more bass because they can play all the lower end louder than you can get out of your speakers, but as you suspect you are most likely still not hearing the sound that is part of the null. I think if it was my room, I would just use my subs as I think the only way around this will get to be very expensive(room modifcations) and time consuming.
