Don't run arduino from the terminal like that. It runs the repository version. If you want the downloaded version 1.0.1, use this:
cd /home/user/arduinodirectorywhereunpacked
./arduino
edit: or the way I do it is navigate to that directory using the GUI, right click on the arduino shell script and create a link. Then move the link to your desktop. Then double-click the link to run the new version.
Do not run as root! No sudo! If you have problems, check your user home directory. There is a hidden directory there named ".arduino" that has a "preferences.txt" file. It may have been changed to owner=root in the sudo stuff you tried. If it is, you must change it back to you as the owner.