ahh you are using wipes or fades, thats why its not all stream copy, with the audio and video together or seperate, there wouldnt be any reencoding without wipes but with wipes there are both ways, it's just that when they are combined its doubtfull that the audio will go out of synch, either way if you are going for using those oh-so-pro wipes instead of jump cuts then you ought to use a diff program, maybe vegas.