As the software recommends, all the videos that you try to convert should be playable first in the application. If you can't play them, then install additional codecs, preview the video files and afterward convert the files. I believe this is the issue you've encountered with the files.
Here is the latest version of Magic Encoder: http://eng.enter-tech.com/support/download.php
For additional codecs, download the following codec pack: http://www.cccp-project.net/