Steps to reproduce:
Add multiple different models to be built.
Use the support tool to generate automatic supports
remove supports from various objects/places
click remove supports again to finish the process
click prepare to print
Note that supports were only removed for the previously selected object when prepare to print was clicked not the other objects.
This is one of the main reasons for using simplify3d. I really like the toolpath quality too, but support removal/addition was the real draw for me. Seems like the check is only for the current object rather than iterating through all objects. Should be a simple fix. (hope I didn't curse it!