your version of x64 MPC is using internal codecs. If you want a version that will use the installed codecs, you need to get it from Shark007's
Tools page
Both GOM and VLC also use internal codecs, I do not know how to make them use installed codecs.
The Shark007 software installs 2 Settings Applications. Open each application and choose the SUGGESTED settings checkbox at the bottom. That should fix your pixilation issues in Media Center. This setting can sometimes interfere with mp4 playback and to correct that you would need to go to the SWAP TAB of the settings applications and re-enable Windows Media Foundation.
Also remember, the 32bit settings application only affects 32bit players and the 64bit application controls playback in 64bit players such as Media Center.