Are you using S/PDIF to pass the audio to the amp? If so basically everything is set to pass the audio without changing it ie
Open the config app that comes with sharks vista codec pack and ensure you have all the default settings in the audio tab, ie speaker config same as the output and AC3/DTS pass through for S/PDIF.
You may also need to check the ffdshow audio that you pass everything through it.
Double check that those mkvs are actually 5.1 AC3 using media info
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