Please find a link to a problem I encountered again today that I knew I had reported earlier in the old newsgroup.
Basically, the problem is that all my plug-ins write their settings to one settings file, the file of the plug-in that gets loaded first (I think). This does not preclude the settings from being found again after Rhino has restarted, so it is not a critical bug in that sense. Still, it is strange that settings do not end up in the settings.xml file of their respective plug-ins.
In the link you will find a ZIP file having 2 plug-ins (code and binary) that repeat this behavior in Rhino 5SR4.