The area ids mist be set in noggit and you need the serverside maps generated for you custom map. What needs a changed extractor.
The normal extractor do not handle custom maps. It just ignore them.
We had this issue with ceril on maruum, and it did turn out to be maps serverside. Do a .gps command in game on your custom map. if your zone or area id shows as a zero (unknown) the client wont know what map to pull up and will display the continent map for what map id you are on.We didnt use dungeonmap, just 'normal' map.dbc and areatable