the Green LED keeps flickering like a pules, I am wondering if it meant to do that and could be making the audio choppy,
No the pulsing or "heart beat" is not related to activity. It's just a default pattern the host puts the GPIO LED into to indicate the board is "alive".
I've not come across choppy audio, it either works or doesn't on the monitors I have, (in facts works with all monitors, doesn't work with video capture box (cheap EZCAP)) the only thing I can think of to make it choppy at present is if the display was in higher than 1080p , which it should be capped to but....
