Here is a clear and reproduceable bug that started happening about two months ago, possibly after a quicktime update.
Inserting a new audio track into jit.qt.movie will only add the first 500 ms if it is uncompressed (i.e. quicktime says 'Integer (Little Endian)'). This bug does not occur when the audio codec is 'Apple Lossless'.
The complete audiotrack should be added.
It would be great if someone could confirm.