I have recently tried Importing a photoshop document into After Effects, retaining the layer styles and keeping them edited. All of this has worked fine but it seems a few of my shapes insist on having a black fill... mostly rectangles or squares. It also screws up some of my premade icons using shapes.
I have no fill selected on all the photoshop layers, it just seems like after effects changes them.
Left = Photoshop document Right = After importing into After Effects
Without knowing anything about the layer structure and so on, nobody can tell you anything. The obvious answer would be that you are using a layer style or blending feature that AE doesn't support...
Not all Photoshop layer styles will import. Simple as that. To know exactly what is going on we need to see your Photoshop layer style structure.
Thank you guys for trying to help, I know my question was quite vague.
The answer I found quite by accident...
All the blacked out shape layers on photoshop needed me to hit the 'Rasterize Layer' button. They then imported correctly.