Raspberry PI and Arduino Nano, issues with USB Serial

Hi there

I have a very simple setup with a Raspberry PI (model B) driving a Arduino Nano connected to the USB port of the Raspberry PI.
I'm running the latest Debian Wheezy on my PI, and I am able to see /dev/ttyUSB0
I have made a simple program for my Nano, where it triggers a digital ouput high and low on input "q" and "a".
It works from the Arduino IDE Serial Monitor. (I coded this from my Windows box)
I was unable to trigger the digital output high with a simple "echo q > /dev/ttyUSB0"
Instead my connected relay blinks on all the digital outputs (on/off once and very quickly) in fact no matter what I send to /dev/ttyUSB0 it does this, and it takes about one second from I hit enter, to it reacts.
I can see on the Nano that in receives something as the TX/RX LEDs are blinking.

I then installed the Arduino IDE on the Raspberry PI, and strangely, I was able to get it working from the IDE.
After I have had the IDE running, I was also able to do the "echo q > /dev/ttyUSB0" and it worked as expected.

Yet after a reboot, I'm back to the strange issue again... So I guess the IDE sets something on the serialport or somewhere else?

Can somebody please tell me how I can set the same "settings" from the commandline, so that I don't have to startup the IDE everytime after a reboot?