Manual Comskip after DVR recording?

I recorded a few DVR items that I would now like to remove the commercials from. (I had the remove commercial featured turned off).

When I try to manually run “Plex Commercial Skipper.exe” (comskip) with a Plex/HDHomeRun recorded ts file, I get an error message stating:

“Unsupported codec! Could not open video codec”

I have a proper comskip.ini file in the same directory as the exe. The public build of comskip can read the file.

Am I doing something wrong? Thanks for you help.