You are right about the problem that was Pulseaudio but that was solved in the 1.0 version of it which is the one that 11.10 is using. The other part of the problem is that you need the 1.1.12 version of VLC to make it work correctly with the new version of Pulseaudio. To do this add the following PPA (Which is the only one I have found so far with the 1.1.12):
sudo add-apt-repository ppa:n-muench/vlc
sudo apt-get update to get the new updates. After that just update VLC to the new 1.1.12.
Tested today and all problems related to sync are gone. Should be mention that this is a PPA from a 3rd party source. So if you would like to wait for Ubuntu to update VLC officially you can do that to. For myself I won't go through another version of Ubuntu with the sync problem again.
INFO - https://launchpad.net/~n-muench/+archive/vlc?field.series_filter=oneiric
UPDATE - There is no more the need to add this PPA since in the main repositories the VLC version 1.1.12 has been added. After todays update to the 1.1.12 version of VLC and using Ubuntu 11.10. Most if not all out of sync problems are gone.
Users need to update their Ubuntu to the latest daily updates which should provide the latest version of VLC (the 1.1.12 version). Already tested and all movies I have seen are working correctly.