Recently a Comskip user asked why Comskip could not detect the commercials in a recording.
It turned out that no sound could be decoded although the sound format was correctly detected.
Also the video format was correctly detected but the video was mostly black with some scattered white gray moving rectangles at the top of the video.
After some search the user suggested that the dvr-ms recording may be made from Comcast on MCE.
DRM scrambling of the audio and video has indeed the described effect.
So if Comskip does detect the video and sound format but is not able to decode the actual sound and video then you most probably have copy protected dvr-ms.
And don't ask me to solve that problem as Microsoft is probably not willing to give me the protection keys.