I am not sure but the problem may be that ffmpeg can only cut on a keyframe, this is part of dealing with compressed video. Even broadcast TV is compressed to a degree so you still have keyframes in the video.
You may be experiencing a compound problem, I am only guessing here, that is a combination of the accuracy of the Comskip + the need to cut on a key frame. I think Comskip is conservative and is set to leave a little commercial rather than cut out programming. You can adjust this in settings but then you will likely loose programming.
When I do use Comskip, which is rarely, I leave it set to normal and use Unprocessed TS as my profile since once you encode and compress again the keyframes seem to get larger. I then take that TS file and run it through Avidemux and in a few minutes a recording I make any adjustments to the cutting of commercials. If you play with Avidemux you can get pretty quick at it…I am doing it right now with some recordings from the History Channel…the hardest channel I have found to get the commercials cut from properly due to the fact they mix resolutions in the stream during commercials.
If you don’t want to do any manual editing, which I do because I am archiving these shows, then you may have to deal with little tidbits of commercials to prevent losing programming.
This is my experience, I may be wrong…but I have a rock solid regimen now for removing commercials…even though it has manual editing involved.