Using DGIndex and AviSynth would be a good way to find out if RFF flags are causing the desync. Using the "Forced Film" field operation, and converting the audio to WAV, use this test script:

video = mpeg2source("blah.d2v")
audio = wavsource("blah.wav")
audiodub(video,audio)

If DGIndex reports 99% film I'd expect this script to play in sync in your media player. However, if it's only 75% or so, indicating your source is some kind of weird hybrid, then try it again with "Honor Pulldown" and this should fix it.