I am having similar issues, I am wondering if I messed up something for the paths during the initial install...

example error found:

CONVERT COMMAND: /usr/bin/mencoder '/home/customer/public_html/desiretube.com/video/am18p-357.wmv' -o /home/customer/public_html/desiretube.com/flvideo/12194602851303946832.flv -of lavf -oac mp3lame -lameopts abr:br=56 -ovc lavc -lavcopts vcodec=flv:vbitrate=500:mbd=2:mv0:trell:v4mv:cbp:l ast_pred=3 -srate 22050 -ofps 24 -vf harddup

################################################## ##

Array
(
[0] => MEncoder 1.0rc1-4.1.2 (C) 2000-2006 MPlayer Team
[1] => CPU: Intel(R) Xeon(R) CPU E5420 @ 2.50GHz (Family: 6, Model: 23, Stepping: 6)
[2] => CPUflags: Type: 6 MMX: 1 MMX2: 1 3DNow: 0 3DNow2: 0 SSE: 1 SSE2: 1
[3] => Compiled for x86 CPU with extensions: MMX MMX2 SSE SSE2
[4] =>
[5] => success: format: 0 data: 0x0 - 0x130e4a
[6] => ASF file format detected.
[7] => VIDEO: [WMV2] 320x240 24bpp 30.000 fps 0.0 kbps ( 0.0 kbyte/s)
[8] => [V] filefmt:6 fourcc:0x32564D57 size:320x240 fps:30.00 ftime:=0.0333
[9] => ================================================== ========================
[10] => Opening audio decoder: [ffmpeg] FFmpeg/libavcodec audio decoders
[11] => AUDIO: 32000 Hz, 2 ch, s16le, 48.0 kbit/4.69% (ratio: 6000->128000)
[12] => Selected audio codec: [ffwmav2] afm: ffmpeg (DivX audio v2 (FFmpeg))
[13] => ================================================== ========================
[14] =>
[15] => Exiting...
)

################################################## ##

Return value: Exiting...

Convert Error or converted video is less than 1 kb in size, try upload a big video. If that do not work, verify convert command works on the server.

################################################## ##

I can not find any way inside the admin to check or adjust ffmpeg paths, is there a way to change or to see the paths that are set?

I have another script running that I can see the paths set on a different domain, ( /usr/bin/ffmpeg )so maybe I can update this somewhere?