Arduino Mega Pro (Sprakfun)

I'm using two Arduino Mega pros for a ROV project as a Senior Design Project (Mech. Eng.) One acts as the controller/master and the Arduino on board the ROV (slave) commands the motor drivers. Today when dry testing the system, communication between the two Arduinos failed and I noticed that the master Arduino's FTDI chip and the green LED of the Arduino were blinking rapidly (slave arduino aboard ROV was fine, using the same power source). I powered down the system then connected the Master Arduino to my computer via USB and all was fine. Powered up again with 12V walwart an it worked fine initially but began blinking again, was able to repeat this several times. This setup has worked over the past week flawlessly.

The input voltage was 12.3 V to both Arduinos, when I changed the supply to a 9 V Walwart the problem no longer presented itself.

Could the voltage regulator onboard the Master Arduino be getting too hot with the 12.3V source?

Old post but any ideas?