if you want to download a youtube video as an MP4, make a bookmark using the code below as the URL. when on a youtube page, click that link, and a "download as MP4" link will appear on the right. and download the video manually as mp4 and avoid the issue all together.
Code:
javascript:if%20(document.getElementById('download-youtube-video')==null%20&&%20!!(document.location.href.match(/http:%5C/%5C/%5Ba-zA-Z%5C.%5D*youtube%5C.com%5C/watch/)))%20%7Bvar%20yt_mp4_path='http://www.youtube.com/get_video?fmt=18&video_id='+swfArgs%5B'video_id'%5D+'&t='+swfArgs%5B't'%5D;%20var%20div_embed=document.getElementById('watch-embed-div');if(div_embed)%7Bvar%20div_download=document.createElement('div');div_download.innerHTML='%3Cbr%20/%3E%20%3Cspan%20id=%5C'download-youtube-video%5C'%3E%3Ca%20href=%5C''+yt_mp4_path+'%5C'%3EDownload%20as%20MP4%3C/a%3E%20'+%20%20((navigator.userAgent.indexOf('Safari')!=-1)?'(control-click%20and%20select%20%3Ci%3EDownload%20linked%20file%20as%3C/i%3E)':('(right-click%20and%20select%20%3Ci%3ESave%20'+%20(navigator.appName=='Microsoft%20Internet%20Explorer'?'target':'link')%20+'%20as)%3C/i%3E'))+'%3C/span%3E';div_embed.appendChild(div_download);%7D%7Dvoid(0);