I had this same problem while working on Ubuntu 12.04 LTS. I managed to fix the problem via running it under sudo. Try running it as administrator.
This "fix" is specific to Linux and of no help to anyone on Windows.
Mine is COM3 and that's what I've been using since I started the project.
If the board stops enumerating (and showing up as a serial port) it usually means the ATmega8u2 chip that does the usb to serial work has been damaged. Common reasons are: changing connections while powered or accidentally connecting 12V a pin or shorting something out.
Is the device showing up at all in Device Manager?