I have update mencoder, but now the conversion just stops:
STARTING VIDEO CONVERSION (process_queue.id = 280)

File: /home/gelernl/domains/geleleger.nl/public_html/video/Xtreme-RC-Test.avi
$file_extn = avi
SELECT * FROM `videos` WHERE `video_id`=281
Video id: 281
Video Output File Name : /home/gelernl/domains/geleleger.nl/public_html/flvideo/4ca4238a0b/1243513547929276899.flv$video_flv = Video Output File Name : /home/gelernl/domains/geleleger.nl/public_html/flvideo/4ca4238a0b/1243513547929276899.flv
Find video duration - START/usr/local/bin/ffmpeg -i /home/gelernl/domains/geleleger.nl/public_html/video/Xtreme-RC-Test.avi
FFmpeg version SVN-r18971, Copyright (c) 2000-2009 Fabrice Bellard, et al.
configuration: --enable-libmp3lame --enable-libamr-nb --enable-libamr-wb --enable-nonfree --enable-libfaad --enable-gpl --disable-mmx --enable-shared
libavutil 50. 3. 0 / 50. 3. 0
libavcodec 52.29. 1 / 52.29. 1
libavformat 52.33. 0 / 52.33. 0
libavdevice 52. 2. 0 / 52. 2. 0
libswscale 0. 7. 1 / 0. 7. 1
built on May 28 2009 16:41:45, gcc: 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)
[NULL @ 0x8072730]Invalid and inefficient vfw-avi packed B frames detected
[mpeg4 @ 0x8072730]frame skip 8

Seems stream 0 codec frame rate differs from container frame rate: 30000.00 (30000/1) -> 25.00 (25/1)
Input #0, avi, from '/home/gelernl/domains/geleleger.nl/public_html/video/Xtreme-RC-Test.avi':
Duration: 00:00:30.96, start: 0.000000, bitrate: 879 kb/s
Stream #0.0: Video: mpeg4, yuv420p, 512x384 [PAR 1:1 DAR 4:3], 25 tbr, 25 tbn, 30k tbc
Stream #0.1: Audio: ac3, 44100 Hz, stereo, s16, 192 kb/s
At least one output file must be specifiedDuration (ffmpeg): 30
DURATION: 00:30Create Thumbnail - START

Creating Thumbnail with ffmpeg

/home/gelernl/domains/geleleger.nl/public_html/thumb/4ca4238a0b//281.jpg
/usr/local/bin/ffmpeg -i /home/gelernl/domains/geleleger.nl/public_html/video/Xtreme-RC-Test.avi -ss 00:00:30 -t 00:00:01 -s 320x240 -r 1 -f mjpeg /home/gelernl/domains/geleleger.nl/public_html/thumb/4ca4238a0b//281.jpg/home/gelernl/domains/geleleger.nl/public_html/thumb/4ca4238a0b//1_281.jpg
/usr/local/bin/ffmpeg -i /home/gelernl/domains/geleleger.nl/public_html/video/Xtreme-RC-Test.avi -ss 00:00:05 -t 00:00:01 -s 120x90 -r 1 -f mjpeg /home/gelernl/domains/geleleger.nl/public_html/thumb/4ca4238a0b//1_281.jpg/home/gelernl/domains/geleleger.nl/public_html/thumb/4ca4238a0b//2_281.jpg
/usr/local/bin/ffmpeg -i /home/gelernl/domains/geleleger.nl/public_html/video/Xtreme-RC-Test.avi -ss 00:00:13 -t 00:00:01 -s 120x90 -r 1 -f mjpeg /home/gelernl/domains/geleleger.nl/public_html/thumb/4ca4238a0b//2_281.jpg/home/gelernl/domains/geleleger.nl/public_html/thumb/4ca4238a0b//3_281.jpg
/usr/local/bin/ffmpeg -i /home/gelernl/domains/geleleger.nl/public_html/video/Xtreme-RC-Test.avi -ss 00:00:19 -t 00:00:01 -s 120x90 -r 1 -f mjpeg /home/gelernl/domains/geleleger.nl/public_html/thumb/4ca4238a0b//3_281.jpgCreate Thumbnail with ffmpeg - END
$cmd_convert_v = convert_avi
428 $cmd_convert = /usr/local/bin/mencoder '/home/gelernl/domains/geleleger.nl/public_html/video/Xtreme-RC-Test.avi' -o /home/gelernl/domains/geleleger.nl/public_html/flvideo/4ca4238a0b/1243513547929276899.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
MEncoder SVN-r29328-4.1.2 (C) 2000-2009 MPlayer Team
success: format: 0 data: 0x0 - 0x33f17e
AVI file format detected.
[aviheader] Video stream found, -vid 0
[aviheader] Audio stream found, -aid 1
AVI: ODML: Building ODML index (2 superindexchunks).
VIDEO: [DX50] 512x384 24bpp 25.000 fps 668.1 kbps (81.5 kbyte/s)
[V] filefmt:3 fourcc:0x30355844 size:512x384 fps:25.000 ftime:=0.0400
================================================== ========================
Opening audio decoder: [liba52] AC3 decoding with liba52
AUDIO: 44100 Hz, 2 ch, s16le, 192.0 kbit/13.61% (ratio: 24000->176400)
Selected audio codec: [a52] afm: liba52 (AC3-liba52)
================================================== ========================


It worked fine when I had just PHP5, now I am running suPHP and PHP5-CGI. Is this not compatible?

Exiting...
Return value: Exiting...
UPDATE `process_queue` SET `status`='6' WHERE `id`='280'
ERROR: failed video conversion.