Oh, forgot to post the workaround for non OSS systems.
In VLC switch audio output to OSS.
Starting vlc with:
aoss vlc
should do the trick (at least it did for me).
I have exactly the same problem :( OS: Debian testing VLC Version 0.8.6a before the update it worked very well. However, this might be an issue related to alsa only, because switching to OSS sound solves the problem mostly (some scratch noises still remain). Strangely alsa works with other applicati...