Unless you have changed it the majority of the problem npc's should be race 127 which is for a_shadowed_man which is suppose to be invisible. Sometimes the default settings just don't seem to have the desired effect. The following should fix this issue.
Code:
update npc_types set bodytype = 66, gender = 0, texture = 0, helmtexture = 0, npcspecialattks = 'ABH' where race = 127;