I have encountered an issue where I have lost changes to my printer and application settings when running multiple instances. It appears that the last instance of simplify3d that is closed will overwrite stored settings if they were changed at one point even if it wasn't the last instance instructed to do so.
To demonstrate this if I open two instances of simplify3d and change settings or printers settings and save them in instance #1 then go and change settings and save in them instance #2 and close program instance #2. Then close program instance #1. The changes to saved in instance #2 are lost. It appears that instance #1 is not aware of #2 and doesn't refresh it's settings and actually overwrites any changes that may have happened.
Often I open one instance for each printer I have which is three. I have had it where I was set up a new profile on one instance and had the other instance reset this profile back to defaults.
-Rob