Perhaps you have turned off the visibility of the layers...
Transitions from Premiere Pro are not compatible with AE. Do each shot as a separate dynamically linked AE comp or recreate your transitions in AE.
But I'm such a noob at Ae i've little idea on how to go about "Dynamically linked AE..." I appreciate now Ae is a technical tool which is going to take time to master which is difficult when I had yesterday to send the completed video to the client. Big problems for me are getting generated when I try to import Pr with Ae. Case in point is my Ae created animation being so much bigger than my imported video clip creating this effect: http://i216.photobucket.com/albums/cc53/zymurgy_bucket/misfit-video-clip-langleys-glitch_z pseec728d8.jpg
Spent all day trying to fix this but no joy, I have today to fix this, wish me luck ;-)