Hey, I had the same problem you are having and my solution was simple. The ins/outs are not identified sometimes as ADAT at all on the I/O selection, but rather Analog1.......or Audio 1............instead. Have you tried recording something into Logic setting up the Adat transfer from your Pro Tools rig output? Once your sure that end of the transactions proper, simply use the Analog inputs as the according ADAT track #. I agree that this is horrible, and very poor in Logic's Design, but it should work anyway.
Keep up the good work.