I had this problem for some time now and a fix would be highly appreciated.
I mainly use Handbrake to produce X264 based MKV files. All the handbrake versions I use are directly from John Stebbins's snapshot repo ( https://launchpad.net/~stebbins/+archiv ... -snapshots
The OS I use is Debian unstable, so maybe that's causing some problems.
The problem is that every muxed MKV file (HD or SD, doesn't matter), lacks the fps information and lots of players refuse to play back the files correctly, because of that. Mediainfo just shows 0.00 fps for the contained video.
After remuxing the files with the proper FPS information, using MKVToolnix, all files play flawlessly and Mediainfo shows the correct fps. I encode with constant FPS and had the fps setting on "same as source". The strange thing is that changing the setting to 25 frames per second ( for example for DVD content), didn't change a thing. The output MKV still lacked the fps info, although the fps were always correctly listed in the log files.
If you need any additional information, please let me know.