Hello,
seeking / trickplay (fast forwarding, rewind) doesn't work in mkv records.
As a workaround (and I'm very glad that I found this out) I'm able to use the software MKVtools - http://www.emmgunn.com/mkvtools/mkvtoolshome.html - which repairs the files somehow.
Could you please fix this mkv problem within tvheadend?
edit:
a fix on the device is also:
apt-get install mkvtoolnix
mkvmerge -o old.mkv --compression -1:none new.mkv