Let me drop this thought to the Developers. I was having trouble with a news channel. when MCE removed the commercials, during playback I had to skip back 10 seconds to get the audio back in sync. Only happened on that one channel, of course what I am about to explain probably happened on more channels, I just didn't record those. So watching the live shows on a digital TV, I noticed that the timing was off on the commercial insertion computer. So while cable was at local commercial, the recordings looked ok to HDHomerun, on the digital TV, the commercial happened in the upper Left corner about 60%, while the remainder of the screen had a freeze frame of where we left the national feed.
So working in the TV industry, this is just an error setting at the cable headend that had the incorrect timing settings, size, or resolution. wrong or glitched into the commercial feed computer. HD Home run handled the problem, but the 8 year old Samsung TV could not deal with the wrong resolution or timing jump inserted into the feed. and MCE also struggled with that jump by throwing off the audio portion of the program.
So are pre recorded commercials having this same issue. or timing jumps when a commercial is not inserted into the stream.