Yeah if they are wired out of phase with each other by mistake they will cause null zones with canceled audio at the middle which has the effect of you only hearing the diffuse side sound and no direct sound. I would advise you to avoid using two separate speakers to drive the same channel as you are likely to get several types of sound problems from such a setup. Speakers that have multiple drivers built into them, like the center channel you pulled out, are carefully designed so the sound is in phase and integrated together well and it should sound like a single source. If you are only listening and normal listening levels one small speaker may work fine but you may want to bump the DB up a little as markw suggested.
Also because you are hearing this noise cancel effect which should only happen if the speakers were wired up by you wrong I would suggest you switch one of them so it is reversed ( red to black and black to red). If the problem goes away then one of those speakers may have a phase wiring problem or for some reason they are set out of phase which doesn't sound right.
You can also run the microphone auto calibration mode with each one wired correctly one at a time and see if it detects the phase problem and tells you to swap the phase.
