I'm using MCEBuddy 2.x to skip commercials, it can't handle the recording correctly. I gave them a full episode from Channels DVR recording; they analyze it came back with this comment:
We investigated this some more, the issue is that original recording has corrupted timestamps which is throwing off comskip when it’s remuxed from the original MKV to TS container. It’s a bug with the ChannelsDVR recorder. For now you can skip remuxing and it should work but ideally report it to ChannelsDVR so they can fix the recording software to create a compliant video without errors.