How to change the shader settings if the red/cyan images are reversed-
if your rendered anaglph Image doesn't look right you may need to reverse the rgb front and back combinations?
The following example shows the original front and back blend combination for the anaglyphcolor.fx.
//Original-Combine front and back
front.r = (front.r * 1.0) * front.a;
front.g = (back.g * 1.0) * front.a;
front.b = (back.b * 1.0) * front.a;
Change the above to-
//Reversed-Combine front and back
front.r = (back.r * 1.0) * front.a;
front.g = (front.g * 1.0) * front.a;
front.b = (front.b * 1.0) * front.a;