CS 6 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. I tried serveral different turtioals, but finally found one that seemed to work pretty good. (BTW if you have a favorite turtorial that you like on keying, please share.)
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 help. BTW the same file exports fine as long as I do not send any of the footage to after effect
I hop you guys can help because 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.

I failed to mention that I tried this on another computer as well with a completly different lesson. This time I brought the whole footage in to afteraffects and did the keying and then went back to CS6 and tried to render it, and it locked up my second computer the same way.

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    I failed to mention that I tried this on another computer as well with a completly different lesson. This time I brought the whole footage in to afteraffects and did the keying and then went back to CS6 and tried to render it, and it locked up my second computer the same way.

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