Same Commercials get Through all Channels

You can could try to customize your comskip.ini using the INIEditor (copy the comskip.ini and editor into a new folder and then customize it rather than customizing the stock ini) and then your conversion task to use the custom comskip ini.

Things that pop out to me:

  1. Try making it more aggressive by enabling Scene change, Closed captions and Cut Scene in the Comskip editor
  2. If you have long running commercials try increasing the max_commercialbreak and max_commercial_size durations