4 seconds is way to short. Infact MCEBuddy won’t even cut commercials if they’re smaller than 20 seconds by default. You can this setting in the system settings page but I would not recommend making it smaller than 10 seconds as it can have other side effects.
Now coming to Comskip, check out the tuning Comskip guide to get started. There’s an easy to use Comskip ini editor app included to adjust the Comskip ini that explains each of the settings in the ini file and impact it has on commercial detection. The job of Comskip is to detect commercials and tell MCEBuddy where they are located for MCEBuddy to then further process them. That’s all Comskip does.