After Effects is centering all layers when importing photoshop files?

To expand on what Rick's reply:

If you've arleady used import "As Composition - Retain Layer Sizes", just open the Comp that was created by After Effects rather than create a new comp and drop the imported layers to it.

Let's say your layereed Photoshop document is called "cunningham.psd".  After importing it as a Composition, you'll see a folder named "cunningham Layers" and a Composition named "cunningham".  Open that Composition.

You may need to change the duration and frame rate of the Composition that After Effects creates, but layers should register correctly.

Cuando importes el archivo de Photoshop y te aparezca esta ventana, elige estas opciones y listo.

You need to open the composition that After Effects creates when you "import as a composition" for the comp to maintain the proper layout.

When you retain layer size, which is the most useful way to set up a project that is going to have a bunch of layers, the Anchor Point of each layer will be in the center of the layer and the layer size will be the same size as the content on that layer. This is also an advantage. 

You are running into a problem because you are not following the proper workflow. 

You should probably also do some research on preparing images and illustrations (Photoshop and Illustrator) for video. The rules are a lot different than preparing artwork and images for print or the web.