CX-5100 do Atmos, CX-5000 do front & Rear presence speakers ( 11 output ) Trust me I have both.
That's what I said too, that the A5100 does Atmos but not the A5000. In the thread title you mentioned Atmos but your issue seems to be with the A5000, so I wasn't totally sure which model you have. Sound like you have both?
There is one more thing to check, that is, the BAL/UNBAL selector switches at the back of the MX-A5000 power amplifier. Perhaps by chance you have had the last two channels set to BAL while the other 9 set to UNBAL or vice versa. Obviously if you are using say UNBAL RCA then all of them have to be set to UNBAL.
Since you have already confirmed all speaker connections are fine, so if the connections between the preamp and the power amp are also good then there I would suggest the quickest way to eliminate any hidden incorrect setting is to do a factory reset. By resetting the unit to factory default condition, unless the unit is defective (highly unlikely), YPAO should recognize all 11 channels.
One question though, does the CX-A5000 has a speaker configuration setup screen where you have to tell the unit whether you have those rear presence speakers, or it detects the preamp to amp to speaker connections automatically? The manual does not seem clear about this.
