Wow. I've had this problem for ages... and only now decided to see what the problem was. I'm using A/52 over S/PDIF. Every single mkv with DTS can be made to desync. Sometimes it happens 50-60% of the times I try... other times, I'll skip around 8 or 9 times until it finally desyncs. But every mkv I have ever watched will desync within 10 or attempts (timeline changes).
Sync is restored by rewinding a bit, jogging, or changing the audio output to another device and back again.
I always have fixed it by clicking on the timeline a few seconds earlier. Often, it doesn't work, and I have to go back and forth two or three times to resync. Occasionally, it will alllllllmost sync-- but it'll be off by an annoying fraction of a second. I spend 10-15 seconds watching lips, rather than watching the movie, just to see if it is correctly sync'd.
I just now tried the audio device "fix." That appears to work very well, but unfortunately, I miss about 5 seconds of dialogue while jumping between the devices.
In my testing, it's not just jumping forward that causes the desync'ing. It can happen in either direction. It can also happen when holding down the forwards or backwards buttons.... basically any skipping/movement of the timeline can throw the audio out of sync.