That's odd. I still don't understand how it could be connected to Natural Desktop, though. It literally doesn't install any system files, the only thing it does is download weather from the internet. The only files it touches are inside its own directory. You can check this for yourself by looking at the install log (C:\Program Files\Stardock\SDCentral\Installed\nd.log, if you use Stardock Central, probably install.log if you do not)
What is the "Script change popup" that you mentioned - some kind of script monitoring system?