Footage captured without audio

I'm hoping someone might be able to enlighten me with possible causes of the following issue.
I've been capturing Digi Beta via Kona LH onto an internal drive (not the system drive) as Apple Pro Res HQ PAL. Even thought 2 stereo tracks have been captured, there is no audio on them, but there is audio on the tape.
The same computer has captured to an external FW800 drive without any issues using the same capture settings, also the same since when capturing direct to Fibre optic SAN. Unfortunately due to a crashing problem, I've clean installed Final Cut on the system again so I can't trace much info.
Any thoughts or advice on would could have occurred would be appreciated.
Specs- Intel Quad Core Mac Pro OSX 10.5.8, running Final Cut Pro 6.0.4.

What is your video connection from DigiBeta to the Kona?
SDI or Component?
What is your audio connection from DigiBeta to the Kona?
AES/EBU or Analog or are trying to embed it in the SDI?
Check you AJA control panel to verify where it thinks the audio should come from.
If the source is embedded audio in SDI, make sure the deck is set to send out audio on the SDI cable.
If you did capture audio, you should see levels bouncing on your FCP audio level meter and make sure they show a waveform in the viewer window.

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