If you must run the IDE as root, you probably do not have the correct group assigned to your user. The Ubuntu install does not (did not on my install) add dialout group to your user. If you add dialout group to your user, log out, then log in again, you should have access to the Arduino serial.
sudo usermod -a -G dialout yourUserName
Here is another thread on this:
http://forum.arduino.cc//index.php?topic=160106.0
That user needed to add tty group to the user also. On Ubuntu, I needed to add dialout only.