Say your main .swf file is in the root directory and it uses a loader to load flvplayer.swf which is in a subdirectory. If the path to your .flv isn’t absolute, it will look for the filename in the root directory once it’s been loaded by the main .swf
stop the server, clear the cahce, restart. also make sure if your using a .net server that the file extension is added to the list of files being served.