There’s a difference between Comskip failed and comskip found no commercials. Comskip failed is a critical error and should be reported at www.comskip.org so they can investigate and fix it. If it finds no commercials, that’s ignored by MCEBuddy, as it’s normal operations. Failing isn’t a normal activity. Can you attach a log of one of the failures?
There’s your issue: Comskip can’t recognize the file
2017-07-30T15:11:09 MCEBuddy.AppWrapper.Comskip → C:\Program Files\MCEBuddy2x\working0\Bat Masterson.S03E04.The Rage of Princess Ann.ts: could not open video codec
Once Comskip fixes the bug we’ll update MCEBuddy. You can refer to this thread in your error report to Comskip so we can track it.