Sorry, I just brought in a different source and noticed that Handbrake does indeed also support DTS passthrough.

What it doesn't do is let you load in external audio. Which is something I need to do for some of the DVDs I'm converting - adding an additional language. I suppose I'll remux afterwards with something else.

Regarding the stutter... Check your framerate. Make sure it is set to "same as source." The stutter could be bad frame rate conversion.