MKV files won't play after upgrade to version 6

[zeroth]

I am unable to play any of the videos that I could play prior to upgrading to version 6. Any ideas? Upgraded on Linux box using standalone. Upgrade is working fine just the transcoding settings are not working. Can someone verify their settings from a working version running 6.0?

Problem Description: Video streaming not work. Only says "hlsjs: video not properly encoded" If I download and play locally on the computer the video works and streams from subsonic fine.
Troubleshooting Steps: Made sure Codecs are in the transcode folder. Look at logs. re-installed server from scratch.
Playback Application and version: try to stream from within subsonic. ffmpeg I believe.
Subsonic Version: (copy/paste from the "About" screen in the Subsonic Web Interface)
Server Version: Subsonic Premium, version 6.0 build a7857c, server jetty-6.1.x, java 1.7.0_79, linux 200.4 mb / 1.81 GB
Hardware Platform: Linux
Java Memory Limit:2000 MB
Output from ffmpeg -i: ffmpeg version 0.8.17-6:0.8.17-1, Copyright (c) 2000-2014 the Libav developers
built on Mar 15 2015 17:00:31 with gcc 4.7.2

Last ten log file lines:

[2016-05-03 21:04:07,152] INFO TranscodeInputStream - Starting transcoder: /media/0194/home/z/Subsonic6/transcode/ffmpeg -ss 0 -t 10 -i /media/0194/home/z/www/serveraddress/WWW/Star.Wars.Episode.VII.The Force Awak$
[2016-05-03 21:04:07,212] INFO InputStreamReaderThread - (/media/0194/home/z/Subsonic6/transcode/ffmpeg)
[2016-05-03 21:04:07,212] INFO InputStreamReaderThread - (/media/0194/home/z/Subsonic6/transcode/ffmpeg) Seems stream 0 codec frame rate differs from container frame rate: 180000.00 (180000/1) -> 23.98 (24000/1001)
[2016-05-03 21:04:14,533] INFO TranscodeInputStream - Starting transcoder: /media/0194/home/z/Subsonic6/transcode/ffmpeg -r 1 -ss 828 -t 1 -i /media/0194/home/z/www/serveraddres/WWW/Star.Wars.Episode.VII.The Forc$
[2016-05-03 21:04:14,586] WARN CoverArtController - Failed to process cover art for Star.Wars.Episode.VII.The Force Awakens.2015.720p.BRRip.X264.AC3-EVO: java.lang.NullPointerException
java.lang.NullPointerException
at net.sourceforge.subsonic.controller.CoverArtController$VideoCoverArtRequest.createImage(CoverArtController.java:661)
at net.sourceforge.subsonic.controller.CoverArtController.getCachedImage(CoverArtController.java:263)
at net.sourceforge.subsonic.controller.CoverArtController.handleRequest(CoverArtController.java:133)
at net.sourceforge.subsonic.controller.CoverArtController.handleRequest(CoverArtController.java:106)
at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:875)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:807)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:571)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:501)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:715)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:487)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1093)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:265)
at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107)
at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:275)
at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:166)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:275)

[zeroth]

update: mkv and avi's not working when trying to stream from in browser. Seems like I need special transcoding settings for mkv files for some reason. I can only get mp4 videos playing in the browswer. Odd since all videos worked prior to the upgrade.

[2016-05-03 22:57:42,875] INFO TranscodeInputStream - Starting transcoder: /media/0194/home/z/Subsonic6/transcode/ffmpeg -ss 0 -t 10 -i /media/0194/home/z/www/zserver/WWW/Ip.Man.3.2015.BDRip.x264-ROVERS/Ip.Man.3.2015.BDRip.x264-ROVERS.mkv -s 720x306 -v 0 -b:v 1000k -maxrate 1000k -bufsize 256k -flags -global_header -map 0:0 -map 0:1 -ac 2 -f mpegts -c:v libx264 -preset superfast -c:a aac -b:a 96k -strict -2 -threads 0 -copyts -
[2016-05-03 22:57:45,350] INFO InputStreamReaderThread - (/media/0194/home/z/Subsonic6/transcode/ffmpeg)
[2016-05-03 22:57:45,350] INFO InputStreamReaderThread - (/media/0194/home/z/Subsonic6/transcode/ffmpeg) Seems stream 0 codec frame rate differs from container frame rate: 48.00 (20000000/416667) -> 24.00 (24/1)

[zeroth]

I reverted back to version 5.3. I would love to upgrade since I do have the premium version but I'm unable to get assistance so I'll just wait. This was a big pain in the ass. Seems like there would be a support option for paying customers?

[zeroth]

Update. Evidently there was a transcoder issue. I got version 6 running properly only through a fresh install. But it streams flawlessly now. The standalone updates are no perfect. The windows version is solid and upgraded without any issue.