The battery is an array of 6 AA batteries but they have discharged a bit.
The arduino is a combination of 1 mega and 2 unos.
I have wired the positive lead of the batteries into the vin pin (via a homemade splitter) of each arduino and the ground pin of the battery in to the ground pin of each arduino (again via a homemade splitter).
Reading the article about power the ardunio on the arduino website I expected the on-board regulator to drop the voltage so that the arduino would behave like normal (like on a USB cable).
These are the voltage difference between the following pins:
5v and GND - 2.8v on battery, normal on USB
digital pin (HIGH) and GND - 7.16v on battery, normal on USB
digital pin (LOW) and GND - 4v on battery, -4v on USB