As far as what I've understood, MPC does include some filters. It's not a 100% directshow app like BSP. I understood those filters are generally not codecs, but splitters. You can see the list of those filters in the MPC option dialog.
I understood MPC opens the file, splits the video and audio, then sends them to the directshow graph.
That may be the reason why I had a problem reading mov files in BSP, but not in MPC: the Quicktime Alternative splitter (that BSP uses through directshow) had problems. MPC's internal MPEG4/Quicktime splitter was doing the job fine.
I replaced the Quicktime Alternative splitter with another Quicktime splitter (Nero) and all problems where gone. See the other recent thread about that :
"playing mov files".
So you need to replace the splitter, for the kind of videos you want to read, by another one.
Give us info on your current splitter.