I am experiencing the same/similar bug with the Paranoid flaw. Paranoid debuff is always active, when I actually enter a restricted area, it shows 'Extra paranoid.'
For example the sneak skill shows the following adjustment values when in a restricted area:
-7 Paranoid
-3 Extra Paranoid
And when not in a restricted area:
-3 Paranoid
This is different from how the flaw description reads. If this is working as intended, the flaws description needs updating. Also if working as intended this is terribly balanced. At 'Average' Temperament it results in a cumulative -42 skill points and 0 health regen when NOT in a restricted area. And a whopping -84 skill points when in a restricted area.