No i've checked the entire system and everything is as it should be.
The only problem i came accross was i had a relay in the heated front screen holder when i shouldn't have.
This is the only relay that uses the alternator power out (other than the main power to the starter motor)
I will try and start the car tonight and see what happens.
The first route i took was to call the alarm installers back as they interupted the ignition wire. They checked everything and there was nothing wrong with the alarm.