I have tested the application, and based on the data added I can say that it sorts the file normally. Basically, the order of the added files in the first step will be stored and used to rename the output files. Additionally, if you're running an operating system higher than Windows XP, right-click the software and choose Run as Administrator.
Secondly, change the output path to another partition and use the filters offered in the Rename/resize window. I have tested this, and it works normally.