In Tivo Desktop, uncheck the box that allows for faster transfers, and then transfer the show again from the Tivo.
What version is your copy of VideoReDo at? (Click 'Help' -> 'About VideoReDo')
You may have a version that doesn't 'play nice' with files downloaded using the faster transfer method.
You can get the latest version (beta) of VRD TS v4 here
I don't know if installing a newer version will affect your trial key, so do so only at your own risk.