The chirps are all the same. This doesn't really point to a mic issue based on the data so far so I'd first confirm that the CC amp and wiring to the CC is functioning by quickly running through the int test tones manually. They should be at pretty similar volumes and sound fairly consistent from FR to CC to FL. If that checks out, my approach would be to do a reset the microprocessor and try Autosetup again.
One more thought-those are unusual and very small speakers so another possibility is the placement of the CC is affecting the acoustic output very adversely. A photo might be helpful.
Edited by SoundofMind - 8/16/13 at 8:45am