I’ve had a similar behavior under 13.10, but I plugged in/plugged out and it usually worked again.
The port is visible as /dev/ttyACM0 as usual, but when I connect to it, there is no data.
When I connect my Pixhawk through USB I don’t get the usual beeping.
This problem is only under Ubuntu. When I run Windows - I have no problems. I connect it and after a few beeps and boops I have it up and running. I can also get it to work under Ubuntu when I connect before the system loads (for example during the GRUB menu).
Any ideas what might be causing this?