adywan said:
Edit:

It's ok i just nominated myself for the biggest dick head award. The original bit for bit recording is fine. I had recently updated the drivers for the soundcard and there's an extra feature that doesn't seem to be linked with the main audio control panel and this one has extra effects. turns out that the problem lay within one of the new filters for playback. In the main panel all effects are disabled but in the new one there was a few new ones that were enabled by default. So the final DVD will have the bit-for-bit laserdisc audio after all. I feel such a bloody idiot :(

I'm just glad you discovered where the problem lay. Reminds me of a similar problem I had a while ago - I couldn't work out why LAME was missing off the first half a second on my MP3 encodes, and it turned out to be a DirectShow filter causing playback problems.