Problem with Twonky and MKV, used to play them

Hi

I have a ReadyNas Duo V1 and use Twonky to play media through My Samsung Smart TV, or well I did.

Went away on holiday for a week, left my sister looking after my house and she used Twonky via my Samsung TV like i showed her.

Anyway, it now only plays AVI files from what I can make out, and seeing as all my media is MKV really this is a problem. I have reset my TV, Reset my NAS installing the firmware again, reinstalled twonky and reset.

I am lost as what to do, I can play the files fine through my computer by accessing them directly from my DUO, but if I try to play them through Twonky vis my computer it will not play them, so I am thinking it is a problem with Twonky itself, but am lost with where to do.

I have started trying to use readyDLNA, but this always gets stuck trying to scan, this is why I started using twonky in the first place.

Thanks

Rich