It is likely the Vertical sync which is the key setting among those you customized. Is this actually the case for you?
In my case I had to change the Power management mode to Prefer Maximum Performance or it would occasionally drop audio whether passthrough was used or not (HTPC Tips and Tricks - #5 by gbooker02). Usually it occurred around black or nearly all black frames. I have a video file where it occurred 3-5 times in the first minute each around an all black screen with some white text to indicate the actors’ names.
