Hi,
on my recent PC with natty 64
$ uname -a
Linux rg 2.6.38-11-generic #48-Ubuntu SMP Fri Jul 29 19:02:55 UTC 2011 x86_64 
x86_64 x86_64 GNU/Linux
$ lshw -c Multimedia
  *-multimedia
       description: Audio device
       product: SBx00 Azalia (Intel HDA)
       vendor: ATI Technologies Inc
       physical id: 14.2
       bus info: pci@0000:00:14.2
       version: 40
       width: 64 bits
       clock: 33MHz
       capabilities: bus_master cap_list
       configuration: driver=snd_hda_intel latency=64
       resources: irq:16 memory:fccf4000-fccf7fff
$ lspci -vv
00:14.2 Audio device: ATI Technologies Inc SBx00 Azalia (Intel HDA) (rev 40)
        Subsystem: ATI Technologies Inc SBx00 Azalia (Intel HDA)
        Control: I/O- Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- 
Stepping- SERR- FastB2B- DisINTx-
        Status: Cap+ 66MHz- UDF- FastB2B- ParErr- DEVSEL=slow >TAbort- <TAbort- 
<MAbort- >SERR- <PERR- INTx-
        Latency: 64, Cache Line Size: 64 bytes
        Interrupt: pin A routed to IRQ 16
        Region 0: Memory at fccf4000 (64-bit, non-prefetchable) [size=16K]
        Capabilities: <access denied>
        Kernel driver in use: snd_hda_intel
        Kernel modules: snd-hda-intel

With system up to date
VLC  1.1.9-1ubuntu1.3 (natty-update)  => I get the audio sync issue as 
described above.
xine is well sync, but just some cracking pb sometime.
Totem 2.32.0 is ok.

I tried the VLC package https://launchpad.net/~bdrung/+archive/ppa
which is not usable at all.

I went back to VLC  1.1.9-1ubuntu1.3 (natty-update)
the issue is back

I installed ALSA drivers from 
https://wiki.ubuntu.com/Audio/InstallingLinuxAlsaDriverModules
version is 2.6.38-11.201108241605
and... everything is just working correctly, still with VLC 1.1.9-1ubuntu1.3. 
sync is ok.
If I uninstall alsa driver, the issue is back, re-install corrects it.

my conclusion:
>> There is something wrong with VLC, because with same config, totem and xine 
>> are ok
>> There is something wrong in snd-hda-intel ALSA driver too, but it is 
>> corrected in last driver.
hardware description:
motherboard ASUS M4A87TD EVO 
Audio chipset VIA VT1818

I have a second PC : Laptop Compaq evo n610c, running natty 32bits
it has integrated 82801CA AC97 audio
kernel module snd-intel8x0
VLC working just fine, sync ok!

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https://bugs.launchpad.net/bugs/805807

Title:
  Sound is not synchronised with the video

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