Vortex formation through the Rossby wave instability (RWI) in protoplanetary discs has been invoked to play a role in planet formation theory, and suggested to explain the observation of large dust asymmetries in several transitional discs. However, whether or not vortex formation operates in layered accretion discs, i.e. models of protoplanetary discs including dead zones near the disc midplane --- regions that are magnetically inactive and the effective viscosity greatly reduced --- has not been verified. As a first step toward testing the robustness of vortex formation in layered discs, we present non-linear hydrodynamical simulations of global 3D protoplanetary discs with an imposed kinematic viscosity that increases away from the disc midplane. Two sets of numerical experiments are performed: (i) non-axisymmetric instability of artificial radial density bumps in viscous discs; (ii) vortex-formation at planetary gap edges in layered discs. Experiment (i) shows that the linear instability is largely unaffected by viscosity and remains dynamical. The disc-planet simulations also show the initial development of vortices at gap edges, but in layered discs the vortices are transient structures which disappear well into the non-linear regime. We suggest that the long term survival of columnar vortices, such as those formed via the RWI, requires low effective viscosity throughout the vertical extent of the disc, so such vortices do not persist in layered discs.