This happens because video that isn't QuickTime DV format must be converted in real time before it is transferred to the FireWire DV converter. This conversion is a very CPU intensive task and may lead to dropouts if the processor cannot handle the stream in real time.
Thus movies output to a FireWire video converter or a DV camera must use the Quicktime DV format. Use iMovie or Quicktime Pro to convert the movie to the appropriate Quicktime DV format for the converter or DV camera you are using.