Here is a hint for the Powder Grangers, if you want to do with the quests surrounding the NCR Prison, don't do the Shootout Quest in Goodsprings until after you have done the Prison Quests. Then go back and do the Shootout part of the Tutorial.
/headdesk Why oh why did I not think of that! :banghead: .
As to why the items are bad karma if you steal them? I use to think its because the jail belongs to the NCR, and thus the items belong to the NCR... However I think it comes down to game mechanics.
There is no marker in game that would allow an item to change its karma tag by doing quests. Thus it is either always marked Bad Karma, or No Karma. If it was no karma then the player who sides with the Powder Gangers would have free range of taking anything you want from them with no repercussions. That is why if you side the NCR stealing from The Legion is bad, and vice versa.
Its the only thing that seems to fit. Later on in the game you can help a group move, and after they are gone you still can't pick up what they left behind, and have no desire to return for.