All the configuration settings are stored in an INI file.

The "Master" INI file is in your program install directory, or, if you pass it a command-line setting to tell it the master is elsewhere, it uses that. After loading the "Master", it checks in your \documents and settings\(username)\application data\PingPlotter directory for PingPlotter.ini and Alerts.ini files. If it finds files there, it uses those as "overrides". The settings from the master get used, but anything that's different in the per-user file gets changed on top of that.

The per-user file will get automatically created if the master is read-only. Once the per-user file exists, all changes made to the user interface are written there. If you delete the per-user file and make sure the master is read-write for your service user (and that it's also read-write for your non-service user), then you should be sharing settings between your service user and your non-service instances.

Hopefully, that clears things up.