I tracked down the problem for Simplify 3D v2.1.0 on my PC (64bit Windows 7).
Didn't matter the profile I used for my FlashForge creator. The built in ones or ones I created, but as soon as I adjusted the "Extrusion Width" AND turned on "Use random start points for all perimeters", my "Prepare" would crash the program every time.
Turning on "Use random start points" and leaving "Extrusion width" at its default setting of .40, worked fine. Changing "Extrusion width" to .45 and leaving Start Points set to "Optimize start points for fastest printing" worked fine.
BUT, changing extrusion width to .45 or .50, AND having "Use random start points for all perimeters" turned on, would crash when I tried to "Prepare" my gcode EVERY TIME.
So if you are getting crashes at the "Prepare" phase, turn off "Use random start points for all perimeters" and report back to use if that fixed your problem.
I spent about 4 hours tracking this down so I am interested to know if anyone else is experiencing this bug.