Hi,
This problem came up last  year. Mikrotik only suggestion was to upgrade the router. I was saw this problem 6.23 then upgraded to 6.27. Now on a different router different place version 6.30.4. Mikrotik had failed to give any explanation why this is happening. I cannot upgrade the router to later versions becaous of pppoe incompatibility with ubiquity devices. Please read what problem is:
When you have 2 routes to same gateway (redundancy) with different distance, they have check-gateway=ping enabled. If one of the route goes down the whole routing table (related to this route) goes unreachable. You cannot ping this gateway, cannot traceroute. Whereas from other side you can ping this router. . Because of this routes become unreachable till you reboot the router. I first saw this problem in december 2015. 

That's the normal thing about check gateway, the gateway with the shortest distance works first.