Here is the stacktrace..

[New I/O server worker #1-7] INFO 20:10:57.916 Starting transcode/remux of mhd-kfp2-720p.mkv
[New I/O server worker #1-7] DEBUG 20:10:57.925 Starting ffmpeg -vframes 1 -i /media/Storage/path/to_video_file/mhd-kfp2-720p.mkv -vcodec copy -f h264 -vbsf h264_mp4toannexb -an -y pipe:
[New I/O server worker #1-7] DEBUG 20:10:57.938 Attaching thread: ffmpeg
[New I/O server worker #1-7] DEBUG 20:10:57.939 Unix process ID (ffmpeg): 10254
[Thread-40] DEBUG 20:10:57.943 FFmpeg version 0.6.2-4:0.6.2-1ubuntu1.1, Copyright (c) 2000-2010 the Libav developers
[Thread-40] DEBUG 20:10:57.944 built on Sep 16 2011 17:00:39 with gcc 4.5.2
[Thread-40] DEBUG 20:10:57.944 configuration: –extra-version=4:0.6.2-1ubuntu1.1 –prefix=/usr –enable-avfilter –enable-avfilter-lavf –enable-vdpau –enable-bzlib –enable-libgsm –enable-libschroedinger –enable-libspeex –enable-libtheora –enable-libvorbis –enable-pthreads –enable-zlib –enable-libvpx –disable-stripping –enable-runtime-cpudetect –enable-vaapi –enable-gpl –enable-postproc –enable-swscale –enable-x11grab –enable-libdc1394 –enable-shared –disable-static
[Thread-40] DEBUG 20:10:57.944 WARNING: library configuration mismatch
[Thread-40] DEBUG 20:10:57.944 libavutil configuration: –extra-version=4:0.6.2-1ubuntu2 –prefix=/usr –enable-avfilter –enable-avfilter-lavf –enable-vdpau –enable-bzlib –enable-libdirac –enable-libgsm –enable-libopenjpeg –enable-libschroedinger –enable-libspeex –enable-libtheora –enable-libvorbis –enable-pthreads –enable-zlib –enable-libvpx –disable-stripping –enable-runtime-cpudetect –enable-vaapi –enable-libopenjpeg –enable-gpl –enable-postproc –enable-swscale –enable-x11grab –enable-libfaad –enable-libdirac –enable-libfaad –enable-libmp3lame –enable-librtmp –enable-libx264 –enable-libxvid –enable-libdc1394 –enable-shared –disable-static
[Thread-40] DEBUG 20:10:57.944 libavcodec configuration: –extra-version=4:0.6.2-1ubuntu2 –prefix=/usr –enable-avfilter –enable-avfilter-lavf –enable-vdpau –enable-bzlib –enable-libdirac –enable-libgsm –enable-libopenjpeg –enable-libschroedinger –enable-libspeex –enable-libtheora –enable-libvorbis –enable-pthreads –enable-zlib –enable-libvpx –disable-stripping –enable-runtime-cpudetect –enable-vaapi –enable-libopenjpeg –enable-gpl –enable-postproc –enable-swscale –enable-x11grab –enable-libfaad –enable-libdirac –enable-libfaad –enable-libmp3lame –enable-librtmp –enable-libx264 –enable-libxvid –enable-libdc1394 –enable-shared –disable-static
[Thread-40] DEBUG 20:10:57.944 libavutil 50.15. 1 / 50.15. 1
[Thread-40] DEBUG 20:10:57.944 libavcodec 52.72. 2 / 52.72. 2
[Thread-40] DEBUG 20:10:57.944 libavformat 52.64. 2 / 52.64. 2
[Thread-40] DEBUG 20:10:57.944 libavdevice 52. 2. 0 / 52. 2. 0
[Thread-40] DEBUG 20:10:57.944 libavfilter 1.19. 0 / 1.19. 0
[Thread-40] DEBUG 20:10:57.944 libswscale 0.11. 0 / 0.11. 0
[Thread-40] DEBUG 20:10:57.944 libpostproc 51. 2. 0 / 51. 2. 0
[Thread-40] DEBUG 20:10:57.951 [matroska @ 0x15b4640]Estimating duration from bitrate, this may be inaccurate
[Thread-40] DEBUG 20:10:57.951
[Thread-40] DEBUG 20:10:57.951 Seems stream 0 codec frame rate differs from container frame rate: 47.95 (48000/1001) -> 24.00 (24/1)
[Thread-40] DEBUG 20:10:57.951 Input #0, matroska, from ‘/media/Storage/path/to_video_file/mhd-kfp2-720p.mkv’:
[Thread-40] DEBUG 20:10:57.951 Metadata:
[Thread-40] DEBUG 20:10:57.951 doctype : matroska
[Thread-40] DEBUG 20:10:57.952 Duration: 01:30:23.96, start: 0.000000, bitrate: 640 kb/s
[Thread-40] DEBUG 20:10:57.952 Stream #0.0(fre): Video: h264, yuv420p, 1280×544 [PAR 1:1 DAR 40:17], 23.98 fps, 24 tbr, 1k tbn, 47.95 tbc
[Thread-40] DEBUG 20:10:57.952 Metadata:
[Thread-40] DEBUG 20:10:57.952 title : Video
[Thread-40] DEBUG 20:10:57.952 Stream #0.1(eng): Audio: ac3, 48000 Hz, 5.1, s16, 640 kb/s
[Thread-40] DEBUG 20:10:57.952 Output #0, h264, to ‘pipe:’:
[Thread-40] DEBUG 20:10:57.952 Metadata:
[Thread-40] DEBUG 20:10:57.952 encoder : Lavf52.64.2
[Thread-40] DEBUG 20:10:57.952 Stream #0.0(fre): Video: libx264, yuv420p, 1280×544 [PAR 1:1 DAR 40:17], q=2-31, 90k tbn, 1k tbc
[Thread-40] DEBUG 20:10:57.952 Metadata:
[Thread-40] DEBUG 20:10:57.952 title : Video
[Thread-40] DEBUG 20:10:57.953 Stream mapping:
[Thread-40] DEBUG 20:10:57.953 Stream #0.0 -> #0.0
[Thread-40] DEBUG 20:10:57.953 Press [q] to stop encoding
[Thread-40] DEBUG 20:10:57.953 frame= 1 fps= 0 q=-1.0 Lsize= 1kB time=10000000000.00 bitrate= 0.0kbits/s
[Thread-40] DEBUG 20:10:57.953 video:1kB audio:0kB global headers:0kB muxing overhead 3.246168%
[mkfifo] DEBUG 20:10:57.994 Starting mkfifo –mode=777 /tmp/ps3mediaserver/1320023457994tsmuxerout.ts
[mkfifo] DEBUG 20:10:58.001 Unix process ID (mkfifo): 10261
[mkfifo] DEBUG 20:10:58.045 Starting mkfifo –mode=777 /tmp/ps3mediaserver/1320023457993ffmpegvideo
[mkfifo] DEBUG 20:10:58.045 Starting mkfifo –mode=777 /tmp/ps3mediaserver/1320023457993videoout
[mkfifo] DEBUG 20:10:58.051 Unix process ID (mkfifo): 10268
[mkfifo] DEBUG 20:10:58.053 Unix process ID (mkfifo): 10269
[mencoder] DEBUG 20:10:58.246 Starting mencoder -ss 0 /media/Storage/path/to_video_file/mhd-kfp2-720p.mkv -quiet -quiet -really-quiet -msglevel statusline=2 -ovc copy -nosound -mc 0 -noskip -of rawvideo -o /tmp/ps3mediaserver/1320023457993ffmpegvideo
[mencoder] DEBUG 20:10:58.253 Attaching thread: mencoder
[mencoder] DEBUG 20:10:58.254 Unix process ID (mencoder): 10277
[mkfifo] DEBUG 20:10:58.296 Starting mkfifo –mode=777 /tmp/ps3mediaserver/1320023457994ffmpegaudio01
[mkfifo] DEBUG 20:10:58.297 Starting mkfifo –mode=777 /tmp/ps3mediaserver/1320023457994audioout
[mkfifo] DEBUG 20:10:58.303 Unix process ID (mkfifo): 10285
[mkfifo] DEBUG 20:10:58.305 Unix process ID (mkfifo): 10286
[mencoder] DEBUG 20:10:58.497 Starting mencoder -ss 0 /media/Storage/path/to_video_file/mhd-kfp2-720p.mkv -quiet -quiet -really-quiet -msglevel statusline=2 -channels 2 -ovc copy -of rawaudio -mc 0 -noskip -oac lavc -fafmttag 0x2000 -lavcopts acodec=ac3:abitrate=448 -af lavcresample=48000 -srate 48000 -quiet -quiet -o /tmp/ps3mediaserver/1320023457994ffmpegaudio01
[mencoder] DEBUG 20:10:58.505 Attaching thread: mencoder
[mencoder] DEBUG 20:10:58.505 Unix process ID (mencoder): 10294
[Thread-59] DEBUG 20:10:58.523 [ac3 @ 0x2a24cd0]frame sync error
[mencoder] INFO 20:10:58.535 Process mencoder has a return code of 1! Maybe an error occurred… check the log file
[linux/tsMuxeR] DEBUG 20:10:58.598 Starting /home/dlogic/pms-linux-1.50.0-SB53/linux/tsMuxeR /tmp/ps3mediaserver/pms-tsmuxer.meta /tmp/ps3mediaserver/1320023457994tsmuxerout.ts
[linux/tsMuxeR] DEBUG 20:10:58.604 Reading pipe: /tmp/ps3mediaserver/1320023457994tsmuxerout.ts
[Thread-43] DEBUG 20:11:00.455 Stopping Unix process 10254: ffmpeg
[Thread-64] DEBUG 20:11:08.601 Stopping Unix process 10300: linux/tsMuxeR
[Thread-64] DEBUG 20:11:08.602 Stopping Unix process 10261: mkfifo
[New I/O server worker #1-7] ERROR 20:11:08.601 There is no inputstream to return for mhd-kfp2-720p