I didn't change anything but SmartPOP2Exchange has reverted all of my settings to default.
Under certain circumstances a third-party virus scanner might prevent SmartPOP2Exchange from accessing the settings files. This results in SmartPOP2Exchange creating a new default settings file.
SmartPOP2Exchange regularly creates backups of the current settings. If your config file has not yet been overwritten it can easily be restored.
To prevent this add the folder which contains the config file (C:\ProgramData\Jam Software\SmartPOP2Exchange) to the exception list of the software that caused the problem. This is also the folder in which the backups are stored.