Ran into this problem. I have a Shape Layer in Photoshop. When the .PSD is imported as a comp, AE CS6 is layering the masks incorrectly. It requires the user to manually re-order the masks to display correctly.
(On a related issue: is there any way to interpret PS shape layers as pixels or Illustrator vectors instead of masks? [without rasterizing in PS, of course] When AE turns them into masks, AE obviously won't update the masks if I make changes to the shape in Photoshop.)
