The change in interval of a few ms could also be because of mp3 binning. Extracting a file of Youtube means you have already been through at least three codecs.
Audio codecs are very good at retaining signal phase as the human ear is very sensitive to errors in this. Whilst I'm not saying it is impossible, I think it would be very unlikely that the interval change is due to transcoding.
Also, as it is a moving receiver this effect is almost expected.