Re: It's the PDX-10...

I had the same problem whit my pdx-10, so I made some test, recording audio on individual channels, on all possible modes and formats.
The result was:
DV SP audio 32K (12bit) both channels captured fine.
DV SP audio 48K (16bit) only captured Ch1.
DVCAM audio 32K (12bit) both channels captured fine.
DVCAM audio 48K (16bit) only captured Ch1.

I captured the material with a Sony GV-HD700 deck, tried material recorded with other cameras, and in all those cases captured both channels fine.

So, if you need both channels, should start recording at 32k, or capture it via the analog output for the old material.