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1b1ed1a
(Get the code!)
The boards produced before "Arduino UNO" (that is the latest version available) uses a different chipset for USB-to-Serial conversion, and shows up as ttyUSB{0,1,2,..}. There were no problems at all with these boards.
The new "Arduino UNO", instead, uses a different chipset and is seen by the kernel as ttyACM{0,1,2...}. It comes out that the RXTX library doesn't consider these ACM devices as serial ports, so the arduino IDE doesn't list them in the menu. The patch to correct this behaviour, AFAIK, is already in the latest RxTX release.
Hope it helps.