Smeck - I saw the exact problem you describe. Was doing this during the Jets game (non HD broadcast), then later in the evening (maybe in between also) on Cold Case in HD. Jets game showed pixel breaks with the audio, Cold Case not. I get my HD via Comcast Cable, not OTA. It is really annoying to say the least, as you sometimes miss key words. Lasts about 2 seconds I would say.
Assassin HTPC + Echo, Sony 49XBR850, McIntosh MX151, MC202, MC7104, MS300, B+W 803D2, CWM's, Janus 1W Sub