Well, they've done something weird in New Vegas. In FO3, merchant's containers were generally always in the same cell as the merchant NPC. In New Vegas - they're in a hidden cell, far removed from prying eyes, that can't be reached by the player.
So the question is, what forces that particular cell to respawn every N days... or is there a script that is misfiring?
thats probarbly it then... that one cell isnt respawning like it should.
hey, could you possibly make a quickie-mod where you put the containers in the merchants cell?
then you can try to see if they respawn like they should.
i cant, since i uninstalled fallout new vegas, but its an interesting theory.