The number one problem I get from people trying to use Fast video indexer is some type of codec related issue. When they finally install the codec they need for the video file everything usually works fine. It used to be so that if windows media player could play a video it could be captured with Fast video indexer. But, in Windows 7 this might no longer be true. I personally discovered this when I got myself a new laptop computer. Windows 7 and windows media player has a number of build in codecs for mp4 that are not direct show based and therefor can not be used with fast video indexer.
So if you can play an mp4 video in windows media player you still might need to install codecs to get it playing in fast video indexer. The best back of mp4 codecs i have found that is free is the ffdshow pack. Just google for it. You might also need the haalii media splitter depending on the file.