May be relevant to anyone with this or a similar situation.
Premiere Pro CS6 recognized only the first mono track, and the audio channels menu had the same.
I used ffmpeg to extract the audio from the file (the cameras DO record everything properly, it IS a Premiere problem).
Put this in a *.bat file:
ffmpeg -i “YOUR FILE NAME” -vn -map 0:a:1 -sn audio_ch2.wav
0:a:0 would be track 1, 0:a:1 is track 2 and so on..
Obviously you should get ffmpeg.exe either in the same folder, or modify the string appropriately to point to it.