In the nitdroid_complete.sh: "echo NOTE: This program should NOT be run as root. echo It has specific parts that need to run as root." What does this mean? confusing huh? What I found out is that... I'm logged in as my own username, but the shell script uses sudo (so the user will be root after the sudo command). There's this $USER variable that refers to the current user. So essentially I'm running part of the script on my username/Desktop while other stuff is running on root/Desktop, one way or another. An easy fix is to replace $USER with your current username in the .sh file. Save and run as: sudo ./nitdroid_complete.sh so everything will be in your own home / Desktop folders.