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:
- Try making it more aggressive by enabling
Scene change,Closed captionsandCut Scenein the Comskip editor - If you have long running commercials try increasing the
max_commercialbreakandmax_commercial_sizedurations
