video problems

[special]

Every time that I convert the audio of my video, the resulting AC3 file is blank/silent. I've converted it with multiple programs to the same result. What's going on here? It can't be a codec issue if I can play the original file, can it?

The audio of the original file is: AAC version 4, 89.2 Kbps

Question 2:
I encoded only the second half of my video. Now I'll have the whole audio file once I can convert it. What's the best way to cut out the first half of my audio, then sync it up with the video?