Could you post a Factory File, or screenshots, those would help a lot. Since it's your first post on the forum, here's what a Factory File is:
4) Factory files – a combined file to retain your entire project
Saving a Factory File picSimplify3D offers a unique way to save all the information about your project into one comprehensive file, known as a “Factory File”. The Factory File includes a copy of the 3D models that have been imported, their positions on the bed, your Process settings, and any custom support material that has been created.
Whenever you exit the Simplify3D Software, the state of the application is automatically saved so that you can easily resume where you left off the next time you open the program. There is no need to save a Factory File each time you close and reopen the program. However, there are other times you may want to save this file such as sharing your project with a friend or creating a back-up for personal use.
To save a Factory File: in the top menu bar, click File > Save Factory File As.
http://www.simplify3d.com/support/tutor ... ile-types/