I've run into this issue too with 12.04 and 13.04 using both OpenJDK 7 and Oracle Java 7. I couldn't convince the patch to compile for 13.04 (kernel 3.8), but will try on 12.04 tonight.
I did discover a consistent work around though.
Place the TX/RX jumpers horizontally for G2533 With the Launchpad uplugged, remove the TX jumper Plug in the launchpad Launch minicom (minicom -D /dev/ttyACM0 -b9600) Put the TX jumper back. If your program is sending data you should see it now. Now launch Energia. You will see an error about ttyACM0 being locked, but you will still be able to upload code.
So far I haven't had any issues doing it this way.