Sorry, but that's just how retain layer size option works. I've found that when I use it, it doesn't take very long to position the layers where I want them.
I expect you're animating the transform properties, so having the anchor points at the center of the layer is good.
In order to maintain position you must open the comp that is created when you import the AI file as a comp retaining layer size. You cannot drag all layers into a new comp and have the layers end up anyplace but in the center of the comp because the anchor points are all in the center of their respective layers.
Thanks Rick, it worked! Much appreciated
Dave: You need to double click on the composition file when its imported, not drag the layers in as I had done before.