You're welcome

I wonder if the slow encoding speed of the app you're using might be triggering the FTP Watcher's upload prematurely, thereby initiating an upload of an incomplete file. The trigger for the Watcher to perform an upload is a new or a changed file - if an existing file's mod date or size changes then it will be uploaded provided the file's new stats remain unchanged for ten seconds. So, if your encoding app doesn't write to the output file for longer than 10 seconds it's possible for this to happen.
Unfortunately, there isn't a preferences setting for this so you can't adjust that value, but I'm going to add a way and send you a build which will, I think, fix the issue by increasing the 'wait' time to something a little more forgiving of the encoding app's speed.
Of course the trade off is that the Watcher's perceived responsiveness to upload files that need it will be decreased but in this case that is probably less important than to someone who makes frequent changes to, or adds, smaller files.