Thanks for your feedback guys.
John and Tick, I think I am in agreement with you guys that I am probably not doing anything wrong and that flex assemblies are just not robust enough.
For a little more insight into what I am doing (or trying to do), I am trying to model an automated cnc assembly line that has a conveyor (the conveyor is just a part file with no movement), 8 instances of the same robot that I want to be able to animate independently of each other and 10 or 12 cnc machines that as of now will not be animated but at some point we may want to simulate their movements as well. My assembly structure is as follows.
AssyLine AssyLineConveyor MachineAssy
For this particular assembly line there will be at least 10 machine assemblies, so MachineAssy01 through MachineAssy10. What I had hoped to do was to set each of the 10 machine assemblies to their Free Drag configurations (which in turn references the robot assembly Free Drag config and is also set to be flexible) and set each one to be Flexible so that while operating in the AssyLine assembly I would be able to move the robots for each machine assembly. As I noted prior this does work but only for a few minutes and eventually the robots quit moving.
The next thing I tried was to dissolve the MachineAssy assemblies incontext of the AssyLine file so that now there are no MachineAssys', now I set the robots to be flexible (the robot is still a sub- assembly) and that seems to work ok so far but I do not like having all this data in the top level AssyLine document. It does not give me the ability to open each machine assembly with that machines robot, electrical cabinet, hyd tank etc..., I have to open the entire assembly line just to work on one machine.
As usual there is always some give and take, it appears that if I want the ability to animate the robots incontext of the assembly line I will need to give up the machine assembly organization...