OK so R:\ is a local RAID Drive??
The log file shows transcoding activity and also you probably have indexing enabled on the library. May be it is just the transcoder that is impacting the system performance
Looking before 08:56
There were two network adapters detected -
Jun 13, 2014 08:29:43:081 [6560] DEBUG - * 12 {8A85A2F9-1884-4E53-B2D6-7BE64F59FC09} (192.168.5.58) (loopback: 0)
Jun 13, 2014 08:29:43:081 [6560] DEBUG - * 19 {EA2E1887-3702-4A89-9136-43C9E98D72CF} (192.168.56.1) (loopback: 0)
Presume the 192.168.56.1 is to do with using a VM ?
At 08:34 started to stream a video which was being transcoded
Jun 13, 2014 08:34:25:938 [4432] DEBUG - Request: [127.0.0.1:31399] GET /video/:/transcode/universal/start.m3u8?path=http%3A%2F%2F127.0.0.1%3A32400%2Flibrary%2Fmetadata%2F2330&mediaIndex=0&partIndex=0&protocol=hls&offset=0&fastSeek=1&directPlay=0&directStream=1&videoQuality=60&videoResolution=1920x1080&maxVideoBitrate=8000&subtitleSize=100&audioBoost=100&session=l0u1s1bonn&X-Plex-Client-Identifier=b3vfdq0dcln&X-Plex-Product=Plex+Web&X-Plex-Device=Windows&X-Plex-Platform=Firefox&X-Plex-Platform-Version=30.0&X-Plex-Version=2.1.12&X-Plex-Device-Name=Plex+Web+(Firefox) (5 live)
Jun 13, 2014 08:34:25:938 [4612] VERBOSE - [IDLE] * http_download - /web/swf/jwplayer/plex.xml - 1 active item(s)
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * mediaIndex => 0
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * partIndex => 0
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * protocol => hls
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * offset => 0
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * fastSeek => 1
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * directPlay => 0
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * directStream => 1
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * videoQuality => 60
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * videoResolution => 1920x1080
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * maxVideoBitrate => 8000
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * subtitleSize => 100
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * audioBoost => 100
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * session => l0u1s1bonn
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * X-Plex-Client-Identifier => b3vfdq0dcln
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * X-Plex-Product => Plex Web
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * X-Plex-Device => Windows
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * X-Plex-Platform => Firefox
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * X-Plex-Platform-Version => 30.0
Jun 13, 2014 08:34:25:938 [4432] DEBUG - * X-Plex-Version => 2.1.12
Jun 13, 2014 08:34:25:939 [4432] DEBUG - * X-Plex-Device-Name => Plex Web (Firefox)
Jun 13, 2014 08:34:25:941 [4432] DEBUG - Using profile Web
...
Jun 13, 2014 08:34:25:945 [4432] DEBUG - [Universal] Using local file path instead of URL: R:\TV\Eureka\Eureka.S03E15.Shower.the.People.mkv
..
Jun 13, 2014 08:34:25:976 [8768] DEBUG - MDE: selected video transcode profile: hls - mpegts/h264/mp3/
...
Jun 13, 2014 08:34:26:026 [4432] INFO - [Transcoder] Stream #0:0: Video: h264 (High), yuv420p, 1280x720 [SAR 1:1 DAR 16:9], 23.98 fps, 23.98 tbr, 1k tbn, 47.95 tbc (default)
...
There were a lot of trancoder errors to do with accessing the temporary transcode area on the C:\ drive in the temp folder C:\Users\Mike\AppData\Local\Temp\
A variety of errors: Access Denied Error, File not found and Access Violation.
Some errors indicate that some process had the area open stopping a deletion. Could windows search indexing or anti virus or could be Plex Media Server bug with parallel processes running impacting each other. You may need to run extra diagnostics to determine what it is eg SysInternals Process Monitor.
Examples:
Jun 13, 2014 08:34:29:893 [2044] ERROR - Failed to delete session directory (boost::filesystem::remove: The process cannot access the file because it is being used by another process: "C:\Users\Mike\AppData\Local\Temp\plex-transcode-l0u1s1bonn-74903b82-ae33-4703-a922-df31edf711d9\media-00001.ts")
Jun 13, 2014 08:35:48:516 [9184] ERROR - Caught exception scanning transcoder directory on file 'media-00033.ts': boost::filesystem::file_size: The system cannot find the file specified: "C:\Users\Mike\AppData\Local\Temp\plex-transcode-l0u1s1bonn-99157d89-0a5a-476c-84ec-ba36f53797d1\media-00033.ts".
Jun 13, 2014 08:35:48:520 [4836] ERROR - Caught exception scanning transcoder directory on file 'media-00039.ts': boost::filesystem::status: Access is denied: "C:\Users\Mike\AppData\Local\Temp\plex-transcode-l0u1s1bonn-99157d89-0a5a-476c-84ec-ba36f53797d1\media-00039.ts".
Jun 13, 2014 08:35:48:523 [9184] ERROR - Caught exception scanning transcoder directory on file 'media-00039.ts': boost::filesystem::file_size: The system cannot find the file specified: "C:\Users\Mike\AppData\Local\Temp\plex-transcode-l0u1s1bonn-99157d89-0a5a-476c-84ec-ba36f53797d1\media-00039.ts".
Jun 13, 2014 08:35:48:524 [8044] ERROR - Caught exception scanning transcoder directory on file 'media-00040.ts': boost::filesystem::file_size: Access is denied: "C:\Users\Mike\AppData\Local\Temp\plex-transcode-l0u1s1bonn-99157d89-0a5a-476c-84ec-ba36f53797d1\media-00040.ts".
Jun 13, 2014 08:35:48:526 [1196] ERROR - Couldn't find the file to stream: C:\Users\Mike\AppData\Local\Temp\plex-transcode-l0u1s1bonn-99157d89-0a5a-476c-84ec-ba36f53797d1\media-00038.ts
Jun 13, 2014 08:35:48:529 [9184] ERROR - Caught exception scanning transcoder directory on file 'media-00045.ts': boost::filesystem::file_size: The system cannot find the file specified: "C:\Users\Mike\AppData\Local\Temp\plex-transcode-l0u1s1bonn-99157d89-0a5a-476c-84ec-ba36f53797d1\media-00045.ts".
Jun 13, 2014 08:35:48:723 [8376] ERROR - Cleaning old transcode directory: C:\Users\Mike\AppData\Local\Temp\plex-transcode-l0u1s1bonn-74903b82-ae33-4703-a922-df31edf711d9
Jun 13, 2014 08:43:31:459 [3692] ERROR - Failed to delete session directory (boost::filesystem::remove: The process cannot access the file because it is being used by another process: "C:\Users\Mike\AppData\Local\Temp\plex-transcode-1GG340053940-8b23a469-b231-4d50-9dd5-9831a12eeb0b\media-00000.ts")
Jun 13, 2014 08:43:31:625 [3692] ERROR - Cleaning old transcode directory: C:\Users\Mike\AppData\Local\Temp\plex-transcode-1GG340053940-8b23a469-b231-4d50-9dd5-9831a12eeb0b
Jun 13, 2014 08:43:31:625 [3692] ERROR - Failed to delete session directory (boost::filesystem::remove: The process cannot access the file because it is being used by another process: "C:\Users\Mike\AppData\Local\Temp\plex-transcode-1GG340053940-8b23a469-b231-4d50-9dd5-9831a12eeb0b\media-00000.ts")
Jun 13, 2014 08:43:31:815 [8196] ERROR - Cleaning old transcode directory: C:\Users\Mike\AppData\Local\Temp\plex-transcode-1GG340053940-8b23a469-b231-4d50-9dd5-9831a12eeb0b
Jun 13, 2014 08:43:31:816 [8196] ERROR - Failed to delete session directory (boost::filesystem::remove: The process cannot access the file because it is being used by another process: "C:\Users\Mike\AppData\Local\Temp\plex-transcode-1GG340053940-8b23a469-b231-4d50-9dd5-9831a12eeb0b\media-00000.ts")
Jun 13, 2014 08:43:31:840 [8196] ERROR - Failed to delete session directory (boost::filesystem::remove: The process cannot access the file because it is being used by another process: "C:\Users\Mike\AppData\Local\Temp\plex-transcode-1GG340053940-8b23a469-b231-4d50-9dd5-9831a12eeb0b\media-00000.ts")