Ok, it took quite a while for me to get back to this thread but I just screened the Russian DVD of Waterloo again last night and this time on my Pioneer Elite Blu-Ray player and did not have the audio sync issues in the second half of the film that I did on the Pioneer DVD player...so maybe this is a player thing and not a DVD thing.
Here is what I did notice though, at the point just before the layer shift the audio goes out of sync for one line of dialogue spoken by Christopher Plummer (playing Wellington, of course) then after the shift the audio was immediately back in sync and remained so for the rest of the film. So, perhaps the audio on the Russian DVD only goes out of sync on some players or upconverting standard DVD players. Obviously, the Pioneer Blu-Ray player also upconverts the picture quality but in this case there was no audio sync problem in the second half of the film. This seems to clearly indicate the audio sync issues are more player related than disc related.
On a final note, this film is gorgeous to look at and we will never see the battle of Waterloo filmed this way again...this really should get full Criterion treatment on Blu as this is a fantastic film that was just harshly judged and ignored at the time. Please Criterion attempt to get your hands on this one!