I had that happen last week on 3 half hour shows. They were all recorded one after the other from the same channe;. I havent noticed it on any other recordings so just assumed that it was a glitch in the broadcast rather than the PVR.
Usually it is the channel or the show itself. When it happens again, try restarting the video or hit the skip back key. The only other way to fix this is via an external device like an AV receiver or a sound bar. Most of those give you the option to a adjust the milliseconds on the fly.