The settings structure of iSMS contains all non-data related information on the program state, such as the methods used, threshold settings, and plot options. In the open-source version of iSMS, the settings structure is initialized in the internalSettingsStructure.m file. The internal settings are overwritten when starting the program by the default settings structure saved to the filepath ../iSMS/settings/default.settings.
The default settings of iSMS can be user-defined and settings can be saved/reloaded from file. When saving sessions, the settings structure is saved with the session.
If you want to restore the initial defaults go to 'File->Settings->Restore internal settings as default'. This will reset the software so that it acts as it did on the first run.