You should post the filter graph or a screen shot of the filters in use for the file.
Also list what codecs you have installed.
The recommend codecs to use are the CCCP codec pack. It is a "swiss army knife" of codec packs; it does just about everything. MKV/x264, DivX, XVID, DVD, even Winwdows Media if you want (not default). For MKV, it uses Haali Media Splitter to read the MKV then ffdshow to decode the x264 inside.
It's recommended to uninstal all other codecs and just run with CCCP.
Personally I dont use ffdshow for x264, I paid a bit and got CoreAvc Professional. I still use the Haali Media Splitter that comes with CCCP, and I use ffdshow for all other codecs as normal, but I deselect x264 in the ffdshow codec list and let CoreAVC handle it. CoreAVC is preferable on older systems, as it uses about 50% less CPU than ffdshow. In my case I use about 30% CPU for a 1080P x264 file with CoreAVC, and about 60% in ffdshow. My HTPC uses slow, silent fans on everything so it runs a bit hot, so I prefer to minimise CPU activity where possible.