Try uploading your AI file so I can take a look.
But you can also do it the old fashioned way:
Enable AICB in illustrator, choosing how you want to copy (I usually choose "Preserve Paths")
Then select the paths and copy them.
Then paste them onto a solid as masks.
Then use this script to convert the masks to shapes:
http://www.redefinery.com/ae/view.php?item=rd_MasksToShapes
Since you say you only have two, you can also manually create a shape layer, manually add a path. Copy/paste one path from illustrator onto the path in AE. Then create another shape path in AE and copy/paste the second AI path to the second AE shape path. Group each separately and add a fill or stroke as needed.
Dan Fredley