So it looks like you have some issues upstream, but nothing that would cause your problem.
So it appears you only have a problem when this is coming from the router, but not through the router. Still leads me to believe some kind of table / memory limit / something is filling up in the router itself. Have you looked into doing the failover with recursive routes instead?
http://forum.mikrotik.com/t/advanced-routing-failover-without-scripting/136599/1