I’ve tested the minimal example on three GPUs: Maxwell Titan X, GTX 1080, and Pascal Titan X.  It fails on all three of them.  The 2d version of this encoder-decoder works just fine, but it would be nice to get it working for the 3d case as well.  Note, this is a very common network construction (just minus the hidden layers), so anyone segmenting 3d data is going to run into this.
For the time being, I’ll just disable cudnn, as suggested.