I have never gotten ffmpegX to convert anything if I couldn't do the conversion with tools built into QuickTime Pro.

I'm having one last stab before ditching the app altogether.
OS 10.3.9, ffmpegX v0.0.9x r2, VLC 0.86f

I can't play or preview the sample file, but it appears to convert. However, it doesn't play in VLC.

ffmpegX v0.0.9x r2
Encoding started on Wed Jun 25 17:48:31 PDT 2008
FFmpeg version CVS, Copyright (c) 2000-2004 Fabrice Bellard
Mac OSX universal build for ffmpegX
libavutil version: 49.0.0
libavcodec version: 51.9.0
libavformat version: 50.4.0
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '/Users/----/Desktop/Sample Movie':
Duration: 00:00:05.0, start: 0.000000, bitrate: 131 kb/s
Stream #0.0(eng), 12.00 fps(r): Video: svq1, yuv410p, 190x240
Stream #0.1(eng): Audio: qdm2, 22050 Hz, stereo
Output #0, flv, to '/Users/----/Desktop/Sample Movie.ff.flv':
Stream #0.0, 12.00 fps(c): Video: flv, yuv420p, 320x240, q=2-15, 200 kb/s
Stream #0.1: Audio: mp3, 22050 Hz, stereo, 56 kb/s
Stream mapping:
Stream #0.0 -> #0.0
Stream #0.1 -> #0.1
bench: utime=1.510s
video:157kB audio:34kB global headers:0kB muxing overhead 2.057145%
Encoding completed on Wed Jun 25 17:48:32 PDT 2008

VLC 0.86f
main debug: CPU has capabilities AltiVec FPU
main debug: looking for memcpy module: 2 candidates
main debug: using memcpy module "memcpyaltivec"
main debug: waiting for thread completion
main debug: thread 42046976 (playlist) created at priority -47 (playlist/playlist.c:184)
main debug: waiting for thread completion
main debug: thread 41968128 (preparser) created at priority -47 (playlist/playlist.c:210)
main debug: looking for interface module: 1 candidate
main debug: using interface module "hotkeys"
main debug: thread 42128896 (interface) created at priority -47 (interface/interface.c:198)
main debug: looking for interface module: 2 candidates
main debug: using interface module "macosx"
main debug: thread 42891264 (manage) created at priority -47 (interface/interface.c:164)
main debug: adding playlist item `Sample Movie.ff.flv' ( /Users/----/Desktop/Sample Movie.ff.flv )
main debug: creating new input thread
main debug: waiting for thread completion
main debug: creating statistics handler
main debug: thread 43161600 (input) created at priority 37 (input/input.c:265)
main debug: `/Users/----/Desktop/Sample Movie.ff.flv' gives access `' demux `' path `/Users/----/Desktop/Sample Movie.ff.flv'
main debug: creating demux: access='' demux='' path='/Users/----/Desktop/Sample Movie.ff.flv'
main debug: looking for access_demux module: 1 candidate
main debug: creating access '' path='/Users/----/Desktop/Sample Movie.ff.flv'
main debug: looking for access2 module: 6 candidates
vcd debug: trying .cue file: /Users/----/Desktop/Sample Movie.ff.cue
vcd debug: could not find .cue file
access_file debug: opening file `/Users/----/Desktop/Sample Movie.ff.flv'
main debug: using access2 module "access_file"
main debug: pre-buffering...
main debug: received first data for our buffer
main debug: creating demux: access='' demux='' path='/Users/----/Desktop/Sample Movie.ff.flv'
main debug: looking for demux2 module: 44 candidates
macosx debug: input has changed, refreshing interface
ffmpeg debug: detected format: flv
ffmpeg error: Seeking too far : EOF?
ffmpeg error: Seeking too far : EOF?
main debug: selecting program id=0
ffmpeg debug: adding es: video codec = undf
ffmpeg debug: adding es: audio codec = mp3
ffmpeg debug: AVFormat supported stream
ffmpeg debug: - format = flv (flv format)
ffmpeg debug: - start time = 0
ffmpeg debug: - duration = -1
main debug: using demux2 module "ffmpeg"
main debug: looking for a subtitle file in /Users/----/Desktop/
main debug: looking for decoder module: 25 candidates
main error: no suitable decoder module for fourcc `undf'.
VLC probably does not support this sound or video format.
main debug: killing decoder fourcc `undf', 0 PES in FIFO
main debug: looking for decoder module: 25 candidates
ffmpeg debug: libavcodec initialized (interface 3349504 )
ffmpeg debug: ffmpeg codec (MPEG Audio layer 1/2/3) started
main debug: using decoder module "ffmpeg"
main debug: thread 43437568 (decoder) created at priority 37 (input/decoder.c:159)
main debug: `/Users/----/Desktop/Sample Movie.ff.flv' successfully opened
ffmpeg error: Seeking too far : EOF?
main debug: EOF reached
macosx debug: input has stopped, refreshing interface
main debug: closing input
main debug: removing module "ffmpeg"
main debug: removing module "access_file"
ffmpeg debug: ffmpeg codec (MPEG Audio layer 1/2/3) stopped
main debug: removing module "ffmpeg"
main debug: thread 43437568 joined (input/decoder.c:191)
main debug: killing decoder fourcc `mp3 ', 0 PES in FIFO
main debug: thread 43161600 joined (input/input.c:412)
main: nothing to play