Arduino won't auto start with RFID shield

I have successfully built one RFID shield and this works fine with Serproxy and Flash, rebooting the PC and it starts up fine everytime. I've now built a second shield which won't startup automatically, I have to do a physical reset using the onboard reset button for it to start working and connecting with Serproxy. I know it is not the shield as i have swapped this onto the original board and it works fine so it must be the Arduino. This is a new board with the ATmega328 chip running on version 15. Any ideas as I'm getting desperate now!