I've been experiencing this issue over the past week or so. Some recorded shows will randomly skip backwards 5-15 seconds at a time. It's very annoying. It appears to be a problem with the recorded file itself, as the same behavior is present on ATV, iPhone and web. Though, it should be noted that on the web player, the video just stops playing and must be skipped ahead or back to resume. However, the exact points of trouble are always the same regardless of playback device.
I haven't been experiencing the problem long enough to understand exactly when/why this occurs but anecdotally, I've noticed the issue on some HDHomeRun Premium TV channels. For example, The Walking Dead on AMC and Gold Rush on Discovery. I'm not sure if this is somehow related but I have also noticed the quality of these problem recordings seem to be very poor (lots of pixelation, blurry SD look and feel).
Not sure what's going on but would love to get it resolved, as the recordings are pretty much worthless in this state.