The Encore structure puts the flv in a "sources" subdirectory under the level with the index.html.
As long as the user has not modified anything, the path should be okay.
Nicolas, confirm that the directory with index.html file also has a subdirectory called "sources," and that that is where the flv/f4v is.
My suspicion for many users with a local, but not web problem, are having a local permissions issue.
One user reported fixing a similar problem by removing odd characters in the filenames. The theory was that the characters were breaking the xml linking.