Your problem is in one tricky option for arduino's com connection. When you reopen COM port where arduino is connected your arduino resets automatically.
Here's workaround from arduino.cc:
DisablingAutoResetOnSerialConnection
The simple way that doesn't require any permanent modifying of your hardware or software configuration changes:
Stick a 120 ohm resistor in the headers between 5v and reset (you can find these on the isp connector too). 120 is hard to find so just combine resistors. Don't go below 110 ohms or above 124 ohms, and don't do this with an isp programmer attached. You can just pull out the resistor when you want auto-reset back.
http://playground.arduino.cc/Main/DisablingAutoResetOnSerialConnection
I hope I was clear enough.