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This desynchronization actually looks to happen because there are black empty frames at the beginning of the tested movie, and these emtpy frames don't get decoded by FFmpeg. Thus the whole movie gets desynchronized (the playback speed is fine).
Question posted the FFmpeg's mailing list to properly handle these frames.
The issue had actually already been reported to the FFmpeg development team (a bit more than one month ago), but still no answer : https://roundup.libav.org/issue2669
Thus this bug clearly depends on FFmpeg's implementation.
This bug does not seem to be still present in the current sfeMovie. The "buggy" OGV movie now plays fine (related to updated version of FFmpeg).