We don't have enough information about your composition to be able to answer your question. Showing screenshots of your Timeline panel and your Composition panel is a good start toward showing us what your setup is.
A picture is nor neccessary for my question.
My comp has 2 layers -
solid as floor has 4 colour gradient
Above that is a circle sitting upon the floor
I have a light shining onto the cirlce to cast a shadow on the floor.
The floor does not accept shadows unless the gradient is switched off.
It seems obvious to me that layers with gradient simply do not accept shadows, its just a limitation of AE however, I wanted a solution to see if there is a workaround. That is all.
As always: In case of doubt, pre-compose. Now your description is a bit vague, but effects normally don't affect 3D rendering, only layer styles do. If you use a gradient overlay layer style, this would be expected. Otherwise you may be introducing the problem somewhere else.
Thanks I precomposed and all is good.
You should also consider creating gradients with a shape layer. It's much more useful than any of the other gradient tools in AE. You can even blend several different gradients to get something like this:
The point is that with a shape layer and multiple gradient fills using different blend modes you can create just about any kind of gradient you want and it will catch a shadow without pre-composing.