I was bringing a layered psd into after effects and trying to preserve the layer structure (i.e. bring it in as a comp, not flattened) I tried every which way I could, and despite selecting comp or comp – original file size, it flattened it every single time! The solution seems to be more of an undocumented feature than a bug, but it’s a fine line: You need the psd to be in rgb. I know that everything should be in rgb regardless, but the weird thing is not that it rejects it (as it would if you brought in other cmyk assets) but that it allows it to go through and mangles it on the way in.
So, keep it RGB, and stay in school!