One thing to make sure is that the following two rules are enabled which honestly there should be no reason for them to be disabled
Code:
Pathing:Fear
Combat:EnableFearPathing
Flee and fear work off of the same logic and it all binds to navmesh. Make sure that you followed the recent instructions in the changelog to make sure you have all of the latest maps and navs and it should work just fine. I did extensive testing with it last night and it was all working smoothly. If you still have issues beyond that we can certainly do more digging