I did not have this problem until the upgrade. I use the official subsonic client on android (running on ICS) with Gallery to play the video. The server is Windows Server 2012 R2, running Subsonic 5.0. I have copied away the packaged codecs, and dropped in the Zeranoe ffmpeg x64 windows daily build, the 3.99.5 x64 rarewares build of Lame, and the 1.3.0 x64 build of Flac. I have been using dailies for a while to improve lag between click and display.
Long story short, it always worked perfectly until the upgrade, now AVI files are streaming through the Android client, but not MKV files.
When I upgraded to 5.0 of subsonic, I shut down the server, installed the software over the existing installation. In troubleshooting, I reinstalled the server and copied over the /subsonic/db folder's contents.
About the ffmpeg dailies - they did not transcode FLAC properly, so I installed FLAC to do that exclusively, no problem.
The server, via a webpage, works fine with this content.
The server is a dual opteron 2360se, 16gb ram, 2 2tb raid 10 arrays on an IBM "real" RAID controller. The passmark score of the system is north of 5,000, and the hard drives are WD Raid Edition 1tb.
If anyone needs access to troubleshoot, please send a private message.
Thanks!