I cant see any difference in the picture myself, but I'll take your word for it. The same VMR9 component is still generating the picture. The only difference is the VRM9 Custom render uses Direct3D to draw the frame to the screen rather than the default method used by VMR9.
Last time I used the VMR9 Custom Renderer it appeared to use less CPU (which was nice) but it also seemed to ignore my video position and scaling numbers in the xml configuration file. I believe the settings where HorizontalOffset, VerticalOffset, HorizontalZoom, and VerticalZoom. Not in front of my computer right now but I believe those are the names of the xml tags. Is the VMR9 Custom Renderer supposed to use those ?