I have the exact same problem when try to make mobs to spawn in an existing map. In my case, Niflheim dungeon F1 and F2. I have created nif_dun.txt with mob spawning script written in npc/re/mobs/dungeons but the map was still empty when I got there. My makeshift solution was puttinh the script in an existing dungeon or field files i.e. file that contains Einbech dungeons and then mob appears normally.
I know this is not a professional way and happy to learn how to make it correctly. Thanks!