I never tried that, I'll try that sometime here soon.
I found out what my initial problem was last night actually. I was trying to convert a 702 meg avi into a valid mpeg2 file. The sound kept being off in different places in the movie. It wasn't universally off or I could have simply fixed it, but the sound would be on in some places and off in others.
I found out it was because of a few bad frames in my avi file and everything seems to be working A-ok now
It's all good ^_^