Also just noticed something interesting after testing with older save games but don't think it has anything to do with Thompson or Stryker but the year - at a certain point it changes from 2142 to 2149 at that point is when it seems that the stores stop working in certain locations - anyone...
I'm having the exact same issue though mine is after becoming Thompson's man go to winds of war and nothing tried Vegas as well same thing. Also tried both through pressing barter key, and dialog - inventory is blank regardless.