When you had the full vs linked clones, did you have the same net number of desktops running on the host? When you are running the test, have you looked at the output form the nvidia-smi command, to see how taxed the GPU actually is?
Outside of that - make sure you are using the VMXNET3 adapter and that interrupt coalescing is functioning properly. That was an issue prior to 5.2 I believe.
When you were talking about frame rate, did you tune this reg key or the PCoIP frame settings: MaxAppFrameRate?