I've noticed that turning option 4 on also activates option 5, which causes items to "duplicate" to 999 and it applies to your stuff as well as stuff on corpses of enemies you kill; e.g. 999 radscorpion poison glands that never go away no matter how many times you "take all".
Soooo I think it must affect your items not 'emptying' properly when they take yer stuff away... If you have option 4 on, be sure to press 5 and deactivate it.
If you don't have this problem, then I gotta figure that it is a bug in the game as similar crap is happening with the BoS Bunker quest where you are also asked to give up your junk...
just like what Mal said turn those off and that should work