I finally did get it to work, I just havent't had a chance to post the solution(s)
I had two issues going on.
Problem 1:
First, one section cut I was trying to create was through the center of the part, this plane was a plane most of the parts where mirrored across.
Solution 1: I offset the section cut .1mm and it worked. Not a "Perfect solution" but it got me some geometry.
Problem 2: I couldn't cut anymore sections, I had cut 5 but Catia wouldn't let me cut anymore. I was cutting through about 25 parts and the drawing size was only around 9megs (at this point).
Solution 2: I loaded Service Pack 5 for Catia V5 r 12, and I was all set.
** Thanks for your help "CATMANDO2" and "puck" I'll be keeping those tips and tricks in mind as I face other issues in the future.