Having the same issue. I can post the plex log, but I believe this is where things are going wrong.
Sep 24, 2015 22:31:54 [0x2ba506401700] DEBUG - Starting a transcode session 3g2tn2irlh4zpvi at offset -1.0 (stopped=1)
Sep 24, 2015 22:31:54 [0x2ba506401700] WARN - WARNING: Couldn't create directory /transcode/plex-transcode-3g2tn2irlh4zpvi-129a71fa-dbd9-4b49-b729-af719709f128
Sep 24, 2015 22:31:54 [0x2ba506401700] DEBUG - [universal] Using local file path instead of URL: /media/TV/Scandal (2012)/Season 5/Scandal.(2012).S05E01.Heavy Is the Head.HDTV-720p.mkv
Sep 24, 2015 22:31:54 [0x2ba506401700] DEBUG - Job running: XDG_CACHE_HOME='/config/Library/Application Support/Plex Media Server/Cache/' XDG_DATA_HOME='/usr/lib/plexmediaserver/Resources/' '/usr/lib/plexmediaserver/Resources/Plex New Transcoder' '-noaccurate_seek' '-i' '/media/TV/Scandal (2012)/Season 5/Scandal.(2012).S05E01.Heavy Is the Head.HDTV-720p.mkv' '-map' '0:0' '-codec:0' 'copy' '-bsf:0' 'h264_mp4toannexb,h264_plex' '-map' '0:1' '-codec:1' 'aac' '-strict:1' 'experimental' '-cutoff:1' '15000' '-channel_layout:1' 'stereo' '-b:1' '258k' '-f' 'matroska' '-avoid_negative_ts' 'disabled' '-map_metadata' '-1' '-' '-start_at_zero' '-copyts' '-y' '-nostats' '-loglevel' 'quiet' '-loglevel_plex' 'error' '-progressurl' 'http://127.0.0.1:32400/video/:/transcode/session/3g2tn2irlh4zpvi/progress'
Thanks for this, would jump on to our IRC Channel to help out with debugging this ?