I had a suspicion as to what the problem is - the areas protected, and I was right. Just tested it and on the cyber knight that I made I edited the Medium Cyber Armor so the Areas Protected, instead of saying all, now says Torso, Arms, Legs, Head and now when I equip it, I get +6 armor. I believe FGs only adds the armor value if it's protecting the torso (the assumed target). I have a feeling you'll have this issue with all the armor that says All (there looked to be a few). Even the Bomb Suit from core SW had this issue (think it says Everywhere)
The bad news is with GunbunnyFuFu MIA, I'm not sure when (if?) the base items will be fixed so you might need to edit all the armors that don't work properly with either changing the Areas Protected field or just adding [armor +x] to them