Hi, the same thing was happening to me and was very frustarting…….
just realised that the color mode of my psd file was set to CMYK instead of RGB. I had drawn my layers in Illustrator (CMYK) and then applied Photoshop effects so I ended up with a final PSD file to import into AE, but never noticed that it retained the Illustrator CMYK mode.
After changing the mode to RGB alll layers appear perfectly inside AE, before that it did very funny things….AE should be able to tell you when things like this happened in my opinion…..anyway is always good to check the possible most simple solutions