I`ve had choppy audio 5.1 on VLC (all variants), using a ATI HD4670 over the proper ATI dongle to provide HDMI to my Onkyo AV. XP Pro
It would start at approx 4 minutes and would need to be reset by clicking on the audio tab then device A/52 over S/PDIF.
I`ve finally sorted it after several weeks of trying thanks to a clue from a different thread viewtopic.php?f=14&t=90011
Suggesting to use OpenGL video output for a unrelated problem but maybe a clue, tried it and Bingo I now have continuous 5.1 DD audio.
Why this solves the problem I have no idea.