It’s very easily replicated by creating a new 2d project and following the steps in my OP. I just created a basic project that still has this issue, would you like me to upload it somewhere?
It happens even without an AIDestinationSetter and no movement. If I remove the AstarPath component from my scene, it no longer does this, so it’s tied to that somehow.
It looks like you have gravity enabled. That will make the agent fall down, and then snap back to the navmesh surface when it gets too far away from it.
In the next update, I’ll make sure that gravity is automatically disabled when in 2D mode.
I actually do have gravity turned off. Maybe it didn’t come through in the export, but the issue still remains, so I’m not sure that is the cause of it.
Also, it’s not falling and snapping back as you mentioned. The Z value fluctuates from negative to positive values.
Were you able to run my project and reproduce it yourself?