Please see post here, including screenshot:

http://forums.creativecow.net/readpost/145/861795

I haven't a clue why this is happening. I've done everything correct, it just seems to be some sort of glitch that I cannot figure out as of yet. Right now I'm encoding with the option set to manual for layer break instead of automatic to see if that changes anything. If that doesn't work, then I'm going to try again and not use the automatic transcode setting as maybe that is what is causing it. Just a pain to have to waste 4 hours at a time waiting =(