Very basic setup: 1 plane with a navmesh surface, some agents, and a flocking behavior. Within seconds they are all stuck (stopped). Tried a new project, default settings for everything, same thing happens. Tried it with and without a repeater.
Another odd thing that happens is when they first start moving, half go in one direction, the other half go in the opposite. They seem to become two flocks (until they stop).
It looks like the task is still running and the agents instead just stop. My guess is that they likely don't have a valid position to move towards so that's why they stop. Instead of setting the position directly try doing a NavMeshAgent.SamplePosition to see if the position is valid. If the position is not valid then a new location can be tested that is nearby.
I think that this is related to the flocking algorithm used. The Movement Pack uses flock from this page. I haven't tried it but this page also looks like they have a solution that you could try. This does mean though that you would have to create a new flocking task for it.