Bottom layer is still masking the layers above with opacity
HI, This is my 1st post, so hope I have included everything I need.
Using Illustrator cc - latest updates applied.
Windows version
I have about 20 layers in an illustrator diagram. There is a background layer which is white at present. But I need it to be black. Please see attached, when I place a red square which is the bottom layer over the images. It fades the colours which were once bright. This has stumped me and for clarity, I did not create the full image, so I am not sure if someone has tried to be cleaver with linking stuff. Also, I have tried changing the original layer and also introducing a new layer.
Please see image

