As of Flash 10.1, they have added the ability to add bytes into the NetStream object via the appendBytes method (described here http://www.bytearray.org/?p=1689). The main
Adobe's F4F format is based on MP4 files, are you able to use F4V or MP4 instead of FLV files? There are plenty of MP4 file splitters around but you would need to make sure the timestamps in the files are continuous, maybe the pause happens when it sees a zero timestamp within the audio or video stream inside the file.