Changing the download folder didn't make a difference debonis. I have noticed though, the smaller files that are under 1gb muxe fine, but anything over 1gb will not muxe properly.
For example I just tried to download this video
http://network.wwe.com/video/v35472215 which is 1.73gb. After it muxed the mp4 file size was 420mb which is only the first 13 mins.