Portable apps ideally shouldn’t be stored in
%ProgramFiles%, because from Vista with UAC onwards only elevated apps (i.e. those running as admin) have write access to that location. Since Sumatra expects the settings file to be writeable, it’s quite possible it exhibits the behavior you’re describing.
Also note that if a non-elevated legacy app insists on writing to protected locations such as
%SystemRoot%, UAC Virtualization might kick in and auto-redirect writes to