Well what can I say.
I sat behind a car and was waiting to turn left but I could see my right indicator was flashing, I checked to see if my hazard lights where on... They weren't!
Then it hit home, I had wired both the grounds together on the same relay to get the alarm to flash both lights.... What a tit, for the last week or so I have been driving around like this and no one had noticed.
Simple fix... I cut one of the ground leads last night and will have to buy another relay and do it properly some time soon.