I have a fix that I think is correct but I need your ffmpeg version and command line to test it as you are doing. Thank you.
I'm getting binary same results for demuxing as EAC3TO but I want to test with ffmpeg also.
[RESOLVED] Potential issue with audio demuxing from VOBs
Re: [RESOLVED] Potential issue with audio demuxing from VOBs
Everything seems fine, but I had to recreate the cut VOB with PGCDemux as it was no longer on my hard drive, and to my surprise I was unable to recreate the original issue. 
I'll keep working on my encodes anyway and will update you in a couple days.
I suggest you try with the cut VOB you have. With 'ffmpeg -i track.ac3' alone you should already see the errors I posted, but you can try a full encode with 'ffmpeg -i track.ac3 -c:a pcm_s32le -f wav output.wav'. In my tests the resulting audio track could not be synced to the video due to the errors (as if it was running slower than the original).
I'll keep working on my encodes anyway and will update you in a couple days.I suggest you try with the cut VOB you have. With 'ffmpeg -i track.ac3' alone you should already see the errors I posted, but you can try a full encode with 'ffmpeg -i track.ac3 -c:a pcm_s32le -f wav output.wav'. In my tests the resulting audio track could not be synced to the video due to the errors (as if it was running slower than the original).
Re: [RESOLVED] Potential issue with audio demuxing from VOBs
Everything is fine with ffmpeg and the fixed DGIndexNV now. I will make a slipstream today.
UPDATE: Fixed in slipstream 198.
UPDATE: Fixed in slipstream 198.