No, it's been happening ever since I started using MPC-HC. I just went through ever video output and found only the EVR Custom and EVR SYNC have proper colors but with flicker.
Here are my results:
System Default: No flicker, changed colors.
Old Renderer: No flicker, Changed colors.
VMR 7 Windowed: No flicker, changed colors.
VMR 9 Windowed: No flicker, changed colors.
VMR 7 Renderless: No flicker, changed colors.
VMR 9 Renderless: No flicker, changed colors.
Nulls: Do Nothing.
EVR: No flicker, changed colors.
EVR Custom Press: Flicker, perfect colors.
EVR SYNC: Flickers, Perfect Colors
Haali: No flicker, changed colors.
Mad VR: No flicker, changed colors, crashes.