Have you been able to resolve this issue? I believe the problem is that the fields in the portal are evaluated from the context of the layout's TO, NOT the portal's. So, those fields which are from TOs in between the layout's TO and portal TO will only show one value (the first related value to your PROJ__Project TO).
You should be able to easily fix this by adding additional TOs that contain the fields you need in the portal, and relate them to your portal TO "downstream" from the layout TO (to the right, in your relationships graph). Then, change specify the errant portal fields as from these new TOs. Now these fields will have to be evaluated through the portal TO's context. You should see the correct values as when you tested with the RAQ layout.
I hope I'm making sense and that this helps!