Sorry for double post. The bug is fixed by using FFMpeg to encode the files. However now I am faced with extremely low video quality. I used this thread to try and fix it:

http://forums.buyscripts.in/viewtopic.p ... se+quality

However when I replace that line with the given the video won't play. I increase the video bitrate however the quality does not increase. Is there no way to increase FFMpeg's quality?