This option is located at: Setup Menu > Settings > Misc
There are times when there will be some files left over in your Parts folder. For example, if you are downloading a large RAR/PAR set, you may stop once you have enough PARs. When you click the Stop button, there will be some files in the Parts folder. If you don’t finish downloading those files, or remove the part files, they will remain in the Parts folder wasting space. So, periodically, you should look in the Parts folder and throw away any un-needed files.
If this option is turned on when SuperNZB starts up, the program will count the files in your Parts and Downloads folder, and if the total is greater than zero, it will open the Folder Totals window.