There are not separate switches for "left-rear" and "right-rear". I think you are confusing the front switch labeled "RR" for "right-rear". The "RR" simple stands for "ReaR". Use either the front switch, or the middle row rotary switch to control ALL of the rears. If you have the front switch at "Off", "Low", or "Hi", the rear switch does nothing (when you don't want the kids fooling with it). When you put the front switch on "RR" (rear), then control is transferred to the rear switch, which has Off, Low, Med, High...or off, 1, 2, 3 (I can't remember).
That said, if at any time, you have significantly different flow on the left versus the right, then yes, some of the flaps/doors must be messed up. The driver temp control (red/blue slider) is what controls the doors. If the driver temp slider is anywhere on the "cold" side, the flap(s) should direct all air to the 4 vents in the roof. It will only blow cold air as well (no actual temp blending in the rear). If the slider is anywhere on the "warm" side, the flap should direct all air to the 1 heat output just behind the right second row seat. Again, it will blow on full-heat, so once the rear heats up, I always shot off the rear completely, and let the front maintain temp, so the kids don't start sweating.