MKV video suddenly stops playing after random time - what could this be?

It is possible that your MKV file is corrupted. This is quite a common occurrence and, if not too badly damaged, can easily be repaired using the Meteorite utility. You can download it here: http://sourceforge.net/projects/meteorite/ It is a portable utility, so does not require installation. Simply run it, drag and drop the suspect MKV onto it and wait till it is done. Copy the repaired file onto your USB drive and try it out.

Should this not solve your problem, you will need to provide more info such as: Do you receive any sort of error message when it stops? Do other MKV files play on your home cinema without problems? Does this file work if on a different USB drive? Have you tried it on a different home cinema or TV with USB capability?

UPDATE: Try Meteorite and, if it does not work, perhaps you could obtain some further info on the file that may be helpful using something like MediaInfo: http://mediainfo.sourceforge.net/en and post it here. From your update it sounds like you created the file yourself and, if this is the case, it will be helpful to know the software that you used - MediaInfo will provide the settings.