Quicktime Audio Drop Problem

[flamesong]

I have an HD video which I created with Final Cut Pro v 7 and exported as a Quicktime movie using FCP default settings.

I used a video conversion programme to compress the Quicktime video to MKV for uploading to YouTube as the original MOV file was 3GB.

The QT uncompressed video plays fine in Quicktime and the MKV file plays fine in VLC but I have been asked to provide an uncompressed version for broadcast and when I tried to play the original QT version in VLC, there is momentary drop in audio.

I don't really understand why this is happening because the QT file is the original, the MKV file was produced from it, so surely the MKV file would have inherited any audio flaws - yet the MKV file plays fine. It's quite possible that the uncompressed QT file will play OK in whatever application the broadcaster is going to use but I am left feeling quite anxious that the video will not play properly.