Samsung TV 46C650 and Samsung HT-C5500 functionality

I have a Samsung 46C650 TV and a Samsung HT-C5500 Home Theatre.
Both are connected to my Media Server via Ethernet.
When i play the files direct from my TV, it plays 99% of the files i have.
When i play the same files from my HT, it only plays about 45% of the files i have.

As per the documentation the HT should be able to support the same files as the TV.

Can Samsung not get the functionality right? The whole idea is to use the HT and have surround sound, not down coded to stereo. That is why i bought a SAMSUNG TV and a SAMSUNG HT???
My TV and HT firmware is the latest available for me to download.

I also noticed that Samsung does not support the latest MKVMerge format. This format has been out since the beginning of 2010, any idea when this will be incorporated?

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