I have a similar issue. My plugin does save the settings, however it is unable to load them from disk. I output to a custom INI in the [Project]/Saved/Config/[Platform] directory. The file gets updated when changes are made in the editor, but nothing is read from that file.
I use SaveConfig() to trigger the save, however manually calling LoadConfig() doesn’t appear to fix the issue either. No errors are generated, and the GetIni command returns empty values until an edit is made to the setting.