The frequencies that the sub is reproducing is supposed to be omnidirectional, ie you are not supposed to be able to determine where the sound is coming from. This is only true of 80 Hz and below. What is the crossover point in your AVR? That being said, the room absolutely is accentuating and diminishing certain frequencies from one sub to the other.
Do you have the ability to make measurements? If so, measure the response of the subwoofers individually. This will tell you how the room is affecting the response of each subwoofer.
Also make sure the subs are gain matched according to the sound pressure level at your listening position, not simply having the volume knobs at the same position on their dial. This means taking SPL readings at your listening position, and setting the sub's gain volume knobs where they generate the same SPL as measured by your listening position. You can try different test tones to achieve this, or also use a pink noise (with the mains OFF for that test).
As lovingthehd said, try different phase settings as well. Keep the phase settings that get you the most SPL. If the subs are out of phase, they could be fighting each other.
Make sure the crossover settings on the plate amp are the same. The crossover switch on both subs should be set to 'out', unless you are doing something a bit more manual with respect to bass management.