Hi Kanien,
All of our administration tools ultimately use the same module, nativerd.dll, to make configuration changes. This module checks the timestamp of the configuration file being written to before making any modifications to the file and aborts the commit operation if it detects that the file has been changed since it was last accessed. The resulting effect of this safeguard is that when there are multiple simultaneous configuration write operations through this module, only the changes corresponding to the first operation to call commit will be written on disk. How the failures from the subsequent commits are handled is specific to the application using the module but most will simply surface the error without attempting to reapply the changes.
You can use this module by using our managed configuration API, Microsoft.Web.Administration, or our COM configuration API, Microsoft.ApplicationHost.WritableAdminManager. If your service is using one of these APIs, it will have that behavior. Since notepad does not use our configuration module and simply writes to the file directly, executing "Save" will overwite the configuration file with whatever is in notepad without regard for changes that may have been made to the file since the file was opened in notepad.
I hope this helps.
Thanks