I did have the same problem but managed to sort it out by loading a previous auto saved game. Luckly I hadn't done very much, so wasn't to much of a biggy.
I had the exact same issues you have to but I noticed it only happened when I went to a nomad camp after receiving a call to meet for a mission.
Long story short, if i avoided the camp and did something else, all was fine and dandy.
Seemed the safe area followed me about. Can't think why but anything is possible in this game right now.
I even went about unequiping and equiping weapons and abilities thinking that it might just not be seeing my equipment due to the new patch but nothing worked.
I know it's a long shot and I know you've tried old saved games but you might try reloading an auto saved game and see if you can do anything and progress from there differently. Hell, at this point you can try fudging it but loading several different saved games.
You shouldn't have to, I know, but it may just free up your game.