Ok, so it looks like if I /mvsetspawn to move the spawn point on one of my worlds then World Map creates separate maps for the worlds. Did that on one of my worlds and now that world got a new folder and the map rendering started over.
(The spawn points were not exactly the same but both worlds that were overwriting each other were around 0 ~ 0)
Inside the folder Multiplayer_xxx.xxx.xxx.xxx_null there are now two subfolders: mw-2,1,0 and mw-3,1,-7
If that is all I needed to know to fix this thanks for your help.
And again, love your plugin.