It would appear that if totem(gstreamer) can't decode, or thinks it can't decode a file, then on 64 bit it falls back to the nonsense about installing the i386 packages (which ultimately fail anyway
Maybe? your 'problem' files fall under this current bug - https://bugs.launchpad.net/ubuntu/+s...10/+bug/973014
If so, (or anyway) you can try this for 64 bit,
Otherwise maybe install mediainfo-gui & open your .mkv in it & identify the encoding ect.
sudo mv /usr/lib/x86_64-linux-gnu/gstreamer-0.10/libgstvideoparsersbad.so /usr/lib/x86_64-linux-gnu/gstreamer-0.10/libgstvideoparsersbad.so.bak
Edit - the other thing you can try is to delete ~/.gstreamer-0.10/registry.x86_64.bin