I haven't experience the same non-recognition problem with the Raspberry Pi 3 and Arduino Mega that I'm using. I'm powering the Arduino via a 9v power adaptor so its USB port is just used for serial output to the Pi.
At at guess when the power goes off/on the Arduino will be up and running before the Pi, then when Pi starts logging the Arduino's serial output the Arduino will reboot again (which can be disabled with some hardware mods)
http://stackoverflow.com/questions/16224816/preventing-reset-on-serial-monitor-connect