Maybe this only applies to the DVDRanger prog. in how it deals with demuxing and muxing of blu-ray.
That however is a wild guess on my part, I haven't heard of any out of sync on blu-ray discs.
I have some relatively new movies...say a few months released and haven't seen anything like this.
Perhaps some of the very latest movie releases has something like this.
Although I have my doubts since there would be reports already.