First of all, I did not test if this bug exists in 3.0 because it needs a fresh install. Sorry if it is already solved, but I think it is not.
Problem After installation, the installer suggests to immediately run Simplify3D. However, if the installer was run with sudo (and it usually is) then the Simplify3D application is run as root but with the environment of current user. This is a severe error. It creates the settings file in user directory but makes it read-only on future runs. This makes all settings on subsequent runs to be reverted to the state that they were on the first exit from application. This happens silently and user may even not know he has a problem, blaming developers for not saving settings at all.
Solution At the end of installation, Simplify3D application must run as the user that started sudo, not as root. Or, better yet, it should not be started at all, because you can not deduce proper user every time. There can be rather complicated cases. Running the software from the installer is Window way and does not fit easy into Linux system , where applications run as sudo confer the root rights to apps they run and files they create. In Linux, user should run app for the first time himself, which by the way ensures that user can run the app. Every app in Ubuntu repositories act this way.