no. if the unsynced audio would come from the 25fps -> 24fps, then it would be much much bigger. on a movie like this, it would be minutes.
no, problem might be a whole different thing. you said that you've only placed the audio on it. i guess the sync problem might be just that: no proper sync check. either by waveform or with video.
or
inproper muxing to mkv. mike, please check your mkv file with your project files.
did nobody else notice this? c'mon guys. i wasn't the only one who grabbed it.