Progress made. I stumbled accross this problem solving guide for autowatch online.
http://www.suffolkalarms.co.uk/index_files/Problem_Solving.htm
So ive tested the alarm and discovered it is the ultrasonic sensors triggering. Sounds like the previous owner has somehow muted the siren. Thankfully there is an option to bypass the ultrasonics when setting by double pressing the fob. This has solved the flashing. Only the doors set it off flashing now when alarm is set. I can live with that. The other thing i noticed is this poorly positioned electrical component in the footwell. Anybody identify whats left of it? Dont think its related to the alarm but might be a stock gen6 component? My foot has caught it this morning so i can see why its been damaged.