I am seeing an issue where, after the commercial skip has happened, the audio is delayed behind the video by around 1-2 seconds. If I return to the menu, then play and resume from where it left off, audio is back in sync. This seems to happen around 50% of time commercials have been removed. One observation is that it seems like comskip is doing a good job of breaking the video off as soon as it detects a commercial, but that the audio for the (would be) commercial continues to play for a second or two. The video returns immediately but the audio is then out of sync.
I am running the latest server build (Synology NAS), and Apple TV client.