If commercials aren’t being detected then it’s related to Comskip INI configuration (which defines the rules for detecting commercials). I’m assuming there no failure is conversion and just a detection issue here.
Will need a conversion log file from the the working and non working setups to compare and see what’s going on with your setup. You can find more details about tuning Comskip commercials here: Tuning Comskip and Custom Comskip INI's (Country / Channel specific)