Hi
I have same problem, with Haali media splitter pdvd8 ultra can only decode some mkv and not others.
My solution was to download MPCVideoDec.ax (MPC-HC standalone video filter), copy it to system32, click start->run type regsvr32 c:\windows\system32\mpcvideodec.ax
I find if one filter doesn't work the other takes over. You could try this simple fix, because it is very easy to remove the filter
To remove click start -> run -> type regsv32 /u c:\windows\system32\mpcvideodec.ax to undo changes if you don't want the codec anymore.
NOTE - you will not be able to open mkv directly with the cyberlink player software.
Nice and working solution,
cigolo