I too have found this to be the case.
I upgraded a project from unity 4.6 to unity 5.3 a while ago. And a lot of things broke.
Only now have I tried to fix all the RAIN AI and I have found that the waypoint routes no longer stop at the last point.
I tried to get it working for hours but in the end I created a new scene with a flat plane and a cube AI with a 4 point waypoint route.
I set the simplest AI on the cube to waypoint route “one way” “forward”.
only to find the cube ping pong between the last two points.
I conclude something is terribly wrong with the AI right now.
Any chance you could let me know when this will be fixed or should I try to install an earlier version of RAIN where this isn’t broken?