I had my HVR-1300 back in my machine this morning to check the audio and seems to work ok for me.
I suspect what you're seeing is actually caused by confusion/conflict caused by having the HVR3000 in the same machine. The HVR3000 uses the same chipset and drivers, but without the hardware MPEG2 encoder.
If you've got time, it might be worth seeing if you get audio if you remove the HVR3000 from the machine.