Lots of details on the related UDN thread. In short, Navigation System is not handling properly deep component hierarchies.
I've added a test map for this to AIProject, it's ComponentHierarchyOnNavmesh. All one has to do to repro the bug is to move the red-colored component by typing in new location/rotation/scale.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-20125 in the post.