ok but since the OP said he had a samsung TV, the fact that Twonky "can" under certain circumstances play .mkv is not of any real importance.
Only way resolve issue is 1) to try to get Samsung's latest drivers (I updated mine when I bought my TV (beginning of August) and this did not help. 2) Hope WD releases newer software (people have been waiting quite a while for this). 3) Pay €8 and upgrade to Twonky 7.
Only option 3 can have you enjoying .mkv files on your Samsung TV in half an hour.