New Post: Use meta data channel to select comskip.ini

You can use that metadata filter (Showname filter) to create a separate conversion task for each channel (you can list all the shows here with a ; from that channel.
Then assign a comskip.ini for each conversion task.

Unfortunately channel metadata is something MCEBuddy is not using today, only Showname for filtering. It's something I can keep in mind for future release if other users are interested in it.