Yeah, I've noticed this happening too in the latest software revision. Not sure, but I think it's a software thing, not hardware. If it's bugging you, I'm sure they'll send you a new box if you ask, but if you can live with it, I'd maybe wait for the next software rev, and see if that fixes it. It's definitely annoying, but when it happens, you should be able to either just press play, or pause and play, and it will go back to normal. If it does, and you jump back a few seconds, it should play normally through the spot it just was glitching in. It's weird.
Mine has been doing it for months. Video always stutters, audio sometimes does, sometimes doesn't. Called DISH, they just said it's a known software problem. Didn't offer to do anything about it (glad to see that DHPP money pays off!).
Wife finally got so upset with it we just had DirecTV installed