I’ve had this problem as well. It seems that if you’re using streaming levels and the project isn’t set to rebuild navmeshes during runtime then you can end up with all the levels’ navmeshes on top of each other instead of correctly offset as Chariots mentioned.
I enabled rebuilding and thought it still wasn’t working until I looked in the properties for the RecastNavMesh object generated when building nav meshes and saw that the Rebuild at Runtime check box was still unticked! It seems that the project settings don’t update existing things very well. Checking Rebuild at Runtime in the RecastNavMesh then resolved the issue.
After I had changed the project settings any new RecastNavMeshes were fine.