I love VLC, but this is the primary reason I haven't been using it for DD or DTS movies in lieu of Media Player Classic.
When I set SPDIF passthrough A/52 setting on, when I skip through certain parts of the movies with the seek bar, the audio and video get out of sync.
I find that I can only get real SPDIF passthrough with Waveout32, so that's the audio output module I use.