MRL currently uses create-labs libraries to interface with serial info - They did a great job of normalizing the Java and doing a full build of 6 types (windows 64/32, Linux 64/32 & Mac 64/32)
Unfortunately the current Jar is filtering out ttyACMx which is the identifier for serial devices for Arduino Uno & Mega..
A easy work-around is to make a symbolic link like this :
ln -s /dev/ttyACM0 /dev/ttyUSB0
you might need to chown or chmod the new link to give it the appropriate permissions
After I did that I could connect to a Mega right away !
For the new to linux crowd,
For the new to linux crowd, what GroG means is, In a terminal window, type:
sudo ln -s /dev/ttyACM0 /dev/ttyUSB0
You'll be asked for your linux password. If you get an error that says the file exists, change USB0 to USB1 or some other number till it works. Remember the number you chose. THEN type:
sudo chmod 666 /dev/ttyUSB0
When you start the Arduino service in Linux, you should see a message at the bottom that it found that serial port. Then, under tools, you can select your board, and the serial port. Click the connect button and you're good to go.
I don't want to create a tutorial for this because it's a work-around, and should be fixed soon.
You only need to do this if you have a newer Arduino such as the Uno or Mega2560 that uses /dev/tty/ACMx instead of /dev/ttyUSBx