You are stuck in state=2
Try this
;Artificial Intelligence Script
;Conjured Header
desc = Light Flash
;Triggers
:state=0,activated=1:timerstart,lighton,state=1
:state=1,timergreater=1250:timerstart,lightoff,state=2
:state=1,activated=0:lightoff,state=0
:state=2,timergreater=500:timerstart,lighton,state=1
;End Script
And don't forget the sound for the alarm...
;Artificial Intelligence Script
;Conjured Header
desc = Light Flash With Alarm
;Triggers
:state=0,activated=1:timerstart,lighton,loopsound=audiobank\atmos\alarmhum.wav,state=1
:state=1,timergreater=1250:timerstart,lightoff,state=2
:state=1,activated=0:stopsound,lightoff,state=0
:state=2,timergreater=500:timerstart,lighton,state=1
;End Script