I'm building a combination of a low power Linux server (Pogoplug running Arch Linux) and Arduino (Mini v3) to monitor and log a variety of sensors in my home and serve them on a web page. The Arduino is connected to the server via USB serial.
When I plug in the Arduino mini after the server has booted, /dev/ttyUSB0 appears and I can communicate with the Arduino without a problem.
However, if I reboot the server, /dev/ttyUSB0 is missing after the reboot. I can unplug and replug the Arduino USB to make /dev/ttyUSB0 reappear. But this is not a great solution for a server that will be running 24/7 and should be able to recover from the occasional power outage. I can reproduce the same problem on my Linux laptop running Ubuntu.