That's the default of woe it will automatically appear the emp even if you config your controller so the best things you have to do during beta on your server capture or get the castle's
Non castle holder of agit their emperium will be appear.
If you want totally disable the other castle's you have to follow this
WoE is a server-wide setting, so it's either ON everywhere, or OFF everywhere. To get around this and "turn off" woe in certain castles, this is what you can do:
Edit trunk/npc/scripts_guild.conf and comment out the castles you are NOT using for WoE (put // in front of the line). This turns of all woe functions for that castle. Optional: to remove the warp portal entrance, edit trunk/npc/warps/guild/guildcastles.txt and comment-out the warps into the castles you are not using.
Source : http://rathena.org/wiki/War_of_Emperium#Turn_OFF_WoE_in_Some_Castles