I too have this problem. It seems like the bot (sometimes) can't "find" my villages in the resource balancer, and when it can't, it deactivates them. That only goes for the resource balancer, though. When using the RArmy, SArmy and so on the bot is always able to "find" my villages.
"Resource balancer - village 01 (555|555) id:9999. Could not navigate to city overview. Resource balancer disabled."