There's a trick to get around that problem: just alt-tab until the npc is visible again. If you open the small map, you will see the green dot, but not the merchant in the game. Alt-tabbing makes the dot move into visibility again, you will see the dot moving after every alt-tab. Sometimes the merchants are in a building and you have a chance to get them out with the alt-tab-method.
There is a nother thread about this problem:
http://forums.larian.com/ubbthreads.php?ubb=showflat&Number=348836
