Premiere Pro :: CS6 Locks Up When Encoding Using Modified Files From After Effects?

I have not had any problems until I started trying to use a green screen, which has turned out to be a major pain. Ultra key did a good job, but I kept being told the after affects does a better job. My computer is a PC has 32 Gigs of ram a 4 gig video card, I7. I also just downloaded all the latest updates. I imported an AVCHD file after shooting a 30 min lesson on green screen. Had to do a lot of editing to get all put together so there were lots of cuts and I had alot nested sections so I can resize myself with the background to keep the perspective correct. After I had decent success with keying, though I wish it were better, I tried moving each indivdual video clip over to after effects to key in there. It looked like it might have been a little bit better than the using ultrakey.

Anyways, after taking forever to get all these clip edited in after affects, I wanted to export my completed video so I could see how well it worked. I never got the the chance because no matter what I choose under MPG2 it would lock up around 8%. Even when I tried to get to encode a 2min section of the video, it still locks up. The only way to get out of the program is to force it closed. As I searched for answer to this problem, someone suggested holding he shift key down while you open CS6, but that did not work. BTW the same file exports fine as long as I do not send any of the footage to after effect
 
it would be nice to be able to try and use after affects as well so I can at least see if the final result of the keying is better or not.