I see part of the problem.
Attempting to use software transcoding on a 32 bit Synology is going to bring it squarely to its knees.
Apr 16, 2016 11:46:54 [0xabb35b70] DEBUG - Job running: XDG_CACHE_HOME='/volume1/Plex/Library/Application Support/Plex Media Server/Cache/' XDG_DATA_HOME='/volume1/@appstore/Plex Media Server/Resources/' '/volume1/@appstore/Plex Media Server/Resources/Plex New Transcoder' '-i' '/volume1/homes/uhzyaj/TV Series/Supergirl/Season 01/Supergirl - 01x10.mkv' '-filter_complex' '[0:0]scale=w=min(1280\,iw):h=min(720\,ih):force_original_aspect_ratio=decrease[0]' '-map' '[0]' '-metadata:s:0' 'language=eng' '-codec:0' 'libx264' '-crf:0' '18' '-pix_fmt:0' 'yuv420p' '-maxrate:0' '3879k' '-bufsize:0' '7758k' '-preset:0' 'veryfast' '-x264opts:0' 'cabac=0:8x8dct=1:bframes=0:subme=0:me_range=4:rc_lookahead=10:me=dia:no_chroma_me:8x8dct=0:partitions=none' '-map' '0:1' '-codec:1' 'copy' '-copypriorss:1' '0' '-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/dwnypmljzrn5976mcmsyeewmi/progress'
Apr 16, 2016 11:46:54 [0x9a101b70] INFO - [Transcoder] Input #0, matroska,webm, from '/volume1/homes/uhzyaj/TV Series/Supergirl/Season 01/Supergirl - 01x10.mkv':
  Metadata:
    title           : Supergirl S01E10 - RMTeam, Rapidmoviez.com
    DESCRIPTION     : Encoded By RMTeam, Rapidmoviez.com
    ENCODER         : Lavf56.40.101
  Duration: 00:43:54.07, start: 0.000000, bitrate: 862 kb/s
    Stream #0:0(eng), 3, 1/1000: Video: hevc (Main), yuv420p(tv), 1280x720 [SAR 1:1 DAR 16:9], 23.98 fps, 23.98 tbr, 1k tbn, 23.98 tbc
    Metadata:
      LANGUAGE        : eng
      ENCODER         : Lavc56.60.100 libx265
      DURATION        : 00:43:54.069000000
    Stream #0:1, 1, 1/1000: Audio: aac (LC), 48000 Hz, stereo, fltp (default)
    Metadata:
      ENCODER         : Lavc56.60.100 aac
      DURATION        : 00:43:54.005000000
Apr 16, 2016 11:46:54 [0xabb35b70] DEBUG -  [FFMPEG] Duration: 2634
Apr 16, 2016 11:46:54 [0xabb35b70] DEBUG - Read line, and done: 1
Apr 16, 2016 11:46:54 [0xabb35b70] DEBUG - Started session successfully: dwnypmljzrn5976mcmsyeewmi
Apr 16, 2016 11:46:54 [0xabe23b70] DEBUG - Started universal transcode output thread
Apr 16, 2016 11:46:54 [0xad3ffb70] DEBUG - [TranscodeOutputStream] Input processing thread started at offset 0 for -1 bytes.
Apr 16, 2016 11:46:54 [0xac3ffb70] INFO - [Transcoder] Output #0, matroska, to 'pipe:':
  Metadata:
    plex.duration   : 2634.07
    plex.total_duration: 2634.07
    encoder         : Lavf56.36.100
    Stream #0:0(eng), 0, 1/1000: Video: h264 (libx264) (H264 / 0x34363248), yuv420p, 1280x720 [SAR 1:1 DAR 16:9], q=-1--1, max. 3879 kb/s, 23.98 fps, 1k tbn, 23.98 tbc
    Metadata:
      encoder         : Lavc56.41.100 libx264
    Stream #0:1, 0, 1/1000: Audio: aac ([255][0][0][0] / 0x00FF), 48000 Hz, stereo (default)
Apr 16, 2016 11:46:54 [0xad111b70] DEBUG - Request: [127.0.0.1:60863] PUT /video/:/transcode/session/dwnypmljzrn5976mcmsyeewmi/progress?width=1280&height=720 (19 live)
Apr 16, 2016 11:46:54 [0xad111b70] DEBUG - It took 0.0 sec to serialize a list with 0 elements.
Apr 16, 2016 11:46:54 [0xb1fffb70] DEBUG - Completed: [127.0.0.1:60863] PUT /video/:/transcode/ses
Respectfully,  I suggest you confine yourself to H.264 video.
Additionally,  in the logs you provided,  I see it matching media.   Is this correct?  it’s still indexing new media?
That little Atom CPU is not very strong
Apr 14, 2016 20:54:41 [0xb2d11b70] INFO - Linux version: 3.2.40 (#5644 SMP PREEMPT Wed Oct 28 12:35:52 CST 2015)
Apr 14, 2016 20:54:41 [0xb2d11b70] INFO - Processor        Intel(R) Atom(TM) CPU CE5335   @ 1.60GHz````