Playing this specific file directly on my iPhone in the Plex app works. Video and Audio are fine, no problems.
Here is a detail of the log file:
Oct 31, 2013 13:18:25:232 [1276] DEBUG - [Transcoder] Thread count: 4
Oct 31, 2013 13:18:25:247 [1840] DEBUG - [Transcoder] Input #0, matroska,webm, from 'http://127.0.0.1:32400/library/parts/2254/file.mkv':
Oct 31, 2013 13:18:25:247 [1276] DEBUG - [Transcoder] Stream #0.0, 68, 1/1000: Video: h264 (High), yuv420p, 1920x1080 [SAR 1:1 DAR 16:9]
Oct 31, 2013 13:18:25:263 [1052] DEBUG - [Transcoder] Stream #0.1(ger), 90, 1/1000: Audio: ac3, 48000 Hz, 5.1, s16, 640 kb/s
Oct 31, 2013 13:18:25:278 [1276] DEBUG - [Transcoder] Stream #0.2(eng), 90, 1/1000: Audio: ac3, 48000 Hz, 5.1, s16, 640 kb/s
Oct 31, 2013 13:18:25:278 [1052] DEBUG - [Transcoder] Stream #0.3(ger), 0, 1/1000: Subtitle: dvdsub
Oct 31, 2013 13:18:25:294 [1276] DEBUG - [Transcoder] Stream #0.4(eng), 0, 1/1000: Subtitle: dvdsub
Oct 31, 2013 13:18:25:310 [1052] DEBUG - [Transcoder] Stream #0.5(fre), 0, 1/1000: Subtitle: dvdsub
Oct 31, 2013 13:18:25:325 [1276] DEBUG - [Transcoder] Stream #0.6(dut), 0, 1/1000: Subtitle: dvdsub
Oct 31, 2013 13:18:25:341 [1052] DEBUG - [Transcoder] Stream #0.7(tur), 0, 1/1000: Subtitle: dvdsub
Oct 31, 2013 13:18:25:341 [1276] DEBUG - [Transcoder] Applying output settings.
Oct 31, 2013 13:18:25:357 [4812] DEBUG - [FFMPEG] Duration: 7361.38
Oct 31, 2013 13:18:25:357 [4812] DEBUG - Read line, and done: 1
Oct 31, 2013 13:18:25:357 [4812] DEBUG - Started session successfully: EB8C138D-2793-4647-AA31-431008C92253
Oct 31, 2013 13:18:25:357 [4812] DEBUG - HLS: Building an M3U8 for 7362 total seconds with 3 seconds/segment, target duration of 3.
Oct 31, 2013 13:18:25:357 [1052] DEBUG - [Transcoder] Frames per second is either 23.976025 or 23.976024.
Oct 31, 2013 13:18:25:357 [1276] DEBUG - [Transcoder] Final font scale: 1.500000 (0.750000) -> 1.221429
Oct 31, 2013 13:18:25:357 [1840] DEBUG - [Transcoder] Audio stream info:
Oct 31, 2013 13:18:25:372 [1052] DEBUG - [Transcoder] codec_id : 15003
Oct 31, 2013 13:18:25:388 [1840] DEBUG - [Transcoder] channels : 6
Oct 31, 2013 13:18:25:388 [1276] DEBUG - [Transcoder] bitrate : 640000/128000
Oct 31, 2013 13:18:25:403 [1052] DEBUG - [Transcoder] samplerate: 48000
Oct 31, 2013 13:18:25:419 [1840] DEBUG - [Transcoder] audiogain : 1.00 (256)
Oct 31, 2013 13:18:25:435 [1276] DEBUG - [Transcoder] aacProfile: 1/-99
Oct 31, 2013 13:18:25:435 [4812] DEBUG - [Transcoder] ----> ac3 is not supported
Oct 31, 2013 13:18:25:450 [1052] DEBUG - [Transcoder] Video stream info:
Oct 31, 2013 13:18:25:451 [4812] DEBUG - [Transcoder] codec_id: 1c/1c
Oct 31, 2013 13:18:25:451 [1840] DEBUG - [Transcoder] level : 41/31
Oct 31, 2013 13:18:25:451 [1276] DEBUG - [Transcoder] avg_fps : 24/24
Oct 31, 2013 13:18:25:467 [1052] DEBUG - [Transcoder] profile : 64/4d
Oct 31, 2013 13:18:25:482 [1276] DEBUG - [Transcoder] vfr : 0
Oct 31, 2013 13:18:25:498 [4812] DEBUG - [Transcoder] fps : 23.98/23.98
Oct 31, 2013 13:18:25:519 [1840] DEBUG - [Transcoder] bitrate : 25.79/4.19 mbps
Oct 31, 2013 13:18:25:535 [1276] DEBUG - [Transcoder] height : 1080/720
Oct 31, 2013 13:18:25:535 [1052] DEBUG - [Transcoder] aspect : 0.56(1.00)/0.56
Oct 31, 2013 13:18:25:551 [1840] DEBUG - [Transcoder] segSize : 75.62mbits/seg, 25.21/25.60MBps
Oct 31, 2013 13:18:25:566 [1052] DEBUG - [Transcoder] timebase: 0.02085(1001:48000)/0.00001(0:1000000)
Oct 31, 2013 13:18:25:582 [4812] DEBUG - [Transcoder] ----> Level Failed
Oct 31, 2013 13:18:25:582 [1276] DEBUG - [Transcoder] Configuring output.
Oct 31, 2013 13:18:25:650 [1840] DEBUG - [Transcoder] Output #0, mpegts, to 'C:\Users\ADMINI~1\AppData\Local\Temp\2\plex-transcode-EB8C138D-2793-4647-AA31-431008C92253-9d6581b7-afd3-4ff5-8422-d2f2aa192517-tmp.ts':
Oct 31, 2013 13:18:25:650 [1052] DEBUG - [Transcoder] Stream #0.0, 0, 1/90000: Video: libx264, yuv420p, 1280x720 [SAR 1:1 DAR 16:9], q=10-51, 200 kb/s
Oct 31, 2013 13:18:25:666 [4812] DEBUG - [Transcoder] Stream #0.1(ger), 0, 1/90000: Audio: libmp3lame, 48000 Hz, 2 channels, s16, 128 kb/s
Oct 31, 2013 13:18:25:666 [1276] DEBUG - [Transcoder] The verbose setting is 0 and PLEX_DEBUG is 0.
Oct 31, 2013 13:18:25:705 [1840] DEBUG - Request: GET /video/:/transcode/segmented/session/EB8C138D-2793-4647-AA31-431008C92253/8/00000.ts [192.168.178.72:51177] (5 live)
Oct 31, 2013 13:18:25:705 [1840] DEBUG - Asked for segment 0 from session.
Oct 31, 2013 13:18:27:335 [4812] DEBUG - [Transcoder] Wrote segment 0 (2.83s, 2.83s, 0.30mb)
Oct 31, 2013 13:18:27:350 [1840] DEBUG - Returning segment 0 from session: C:\Users\ADMINI~1\AppData\Local\Temp\2\plex-transcode-EB8C138D-2793-4647-AA31-431008C92253-9d6581b7-afd3-4ff5-8422-d2f2aa192517\media-00000.ts
Oct 31, 2013 13:18:27:350 [1840] DEBUG - Content-Length of C:\Users\ADMINI~1\AppData\Local\Temp\2\plex-transcode-EB8C138D-2793-4647-AA31-431008C92253-9d6581b7-afd3-4ff5-8422-d2f2aa192517\media-00000.ts is 315276.
Oct 31, 2013 13:18:27:683 [1052] DEBUG - Request: PUT /video/:/transcode/session/EB8C138D-2793-4647-AA31-431008C92253/progress?progress=0.0&size=0&speed=1.8&remaining=3998 [127.0.0.1:60299] (5 live)