Fortunately most of what I've tried has AC3 and I've been selecting that.

One thing I've been experiencing when playing the resulting files back is that some of them - not all - will have a slight stutter in the video every few seconds. I don't know what causes it, and it might just be the device I'm playing them back on (the WDTV Live), but it's noticeable. I don't think I see it on my computer, so that could be all it is...