It might be that your mind is convinced that it can trust you system but your instinct is not to. To truly trust your system is a habit change - and how hard it is to change your previous habits depends on how deep they have been engrained.
So in addition to looking at your present GTD implementation for any gaps in the actual system, it might also help to observe and try to work out where your feelings of anxiety come from. Is there anything in your past? Can you pinpoint what specific contexts or events that trigger your insecurity? (no need to answer, just rhetorical questions...)