In this paper we use the CASL method to explore the role of boundary conditions in determining the long-time behaviour of rotating, stratified, quasi-geostrophic turbulence. We find that initially two-dimensional (sufficiently tall) columns of potential vorticity (PV) break down through three-dimensional instability to give a fully three-dimensional flow consisting of ellipsoidal structures. This is the case both for rigid-lid (isothermal) vertical boundary conditions and for vertically periodic boundaries. However, the rigid boundary case gives rise to semi-ellipsoids at both the top and bottom boundaries, and, for sufficient domain depths, preferred depths for the formation of ellipsoids in the interior. By contrast, in the vertically periodic case, the distribution of ellipsoids is homogeneous in depth.