It sounds like it may be an issue with how you linked the file. The FLV Playback that you use to play the FLV still needs the source Movies. I have had an issue where the address the FLVPlayback is looking for is hard-coded to a folder on my computer rather than a relative path from the .swf file. If I were you I would check out the component window in your FLV and make sure the path does not have a long address.

Good Luck!