comskip results will vary by network and show.
Channels DVR devices (clients) all have their quirks when playing back.
I don't use a Channels client device, just the DVR.
If you have issues and like Channels DVR, raise the issue and submit diagnostics.
You can "tune" the comskip that Channels DVR uses, but it's not for the feint of heart and not a simple GUI/switch.
comskip was not developed by the Channels DVR developers.
http://www.kaashoek.com/comskip/