Hello Skinzee,
we have the same “problem” months ago and after some search in this forum I don’t think it’s possible to show devices which are down over more than one submap. Maybe it’s a feature not a bug 
So we have arranged our map structure with this knowing 
http://forum.mikrotik.com/t/need-general-practices-for-n00bs/59303/3
http://forum.mikrotik.com/t/network-map-device-count/49816/4
http://forum.mikrotik.com/t/displaying-submap-outages-on-top-level/32227/2
Sebastian