We usually convert videos to mp4 files for playback on many portable devices, such as iphone ipad ipod, but some of the video converters can not do the process with a stable mode, crash, no sound, audio not coincide with video, etc. That really drives people crazy.So was I.
I used HandBrake before for its open source and good reputation. Yet I was sometimes really pissed off when encountering no sound and out of sync issues after long time conversion finished. Later, I turn to other video softwares for help, and I finally kept MacX Video Converter Pro. I've used it for many formats conversion and no such problems happen again. So I recommed it and hope that solves your problem.
Source: out of sync problem details and solution