The analog versions were coming in as Dolby Digital 2.0, which is a separate mix entirely. I've seen cases where a local affiliate screwed up the HD audio feed while getting the SD audio feed right. Thankfully that's less common now that more people are actually watching the HD broadcasts, as they get lots of calls if they mess things up too bad. I doubt that a hardware fault would affect just those two HD stations. It was most likely either a firmware glitch in the first unit or a broadcast error that got fixed at around the same time as your DVR box swap.