Let me see... clickety-click, MediaCenter 13.0.54, CoreAVC 1.8... piking up some mkv file at random, play. It works.
What's getting used - CoreAVC, CoreAAC, Haali Media Splitter, Haali Media Renderer.
Picking up a different mkv file... CoreAVC, AC3Filter, Haali Media Splitter, Haali Media Renderer; works again.
Give it a run to Graphedit and see what's getting picked up by default, based on DirectShow filters' merit alone. Tweak it with a filter manager if you feel the need. Better yet, configure MC to use certain filters for certain file types (force CoreAVC on it, if haven't already).