As much as I hate to say it, I think it's just bad luck. The one thing I have noticed now, is that when there are 2 characters in the same area wtih Greater Sanctuary, one gets noticed.
Maybe this is just coincidence, but I notice that each time I am in an area with another and both are under Greater Sanc, one will get spotted. This observation stems from events over the past year or so. Granted, before it was seldom that I traveled with another while we were both using Greater Sanc, but maybe something we can look into as players or others have feedback.