I often design everything in Illustrator, then import the file into AfterEffects as a composition, apply "Convert Shapes from Vector Files" to each layer so that I am working with vector, and then animate the new shapes.
However, I just ran into an issue where I convert a compound shape (with solid color), and after I apply "Convert Shapes from Vector Layer", it shows up as transparent. The layer is there, and I can modify the vector points, but I don't see it. When I click on the shape, it still shows white in the Fill. Opacity is at 100%.