I fast travel to the Gun Runner factory like I always do, and the Guard become hostile when I try to buy stuff......what gives?

this has happened to me once too but i think it was because i was wearing a conflicting factions armor... but on the other hand lots of NPCs are attacking me for no reason even when im not wearing conflicting armor. heres the thread i made about this problem http://www.gamesas.com/index.php?/topic/1129049-npcs-attack-for-no-reason/

I was wearing Leather armour........suddenly the Gun Runner just hate people with leather?

yeah sounds like you have the same problem as i do