After running Comskip with the -w switch for DebugWindow, it seems to run OK and produce the Debug and graph window, but the CPU usage remains at 97-97% after Comskip completes. Closing Comskip releases this usage.
Its as its supposed to be because I can't use the windows event mechanism from a console window so I have used busy waiting, busy at decoding at full speed to have a very fast mpeg preview.