I am looking for a simple way to convert a lot of my video collection from MKV/AVI to MP4. Every program I have tried, however, seems to leave sync issues with the audio, even if it's just a bit. I've tried Handbrake, which is supposed to be the simplest, using the "variable framerate" settings (the constant setting screwed it up big time) and "same as source" for FPS, but it still seems to be off .5-1 second, which is unacceptable to me.

What are you using with what settings?