IF you have the Hyper-V role installed in your Windows 8.1 VM, then you are running the Windows 8.1 Vm nested under Hyper-V. That's how Hyper-V works. The management OS runs in a Hyper-V VM. It does not surprise me that the root partition would be slower than a guest partition, and I suspect that the slow boot is probably due to the zeroing of the 8GB of memory. It's possible that Windows 8.1 uses a new memory-clearing loop that we do not recognize, and for which we do not have an optimization. Was this faster with Windows 8.0 as the management OS?
I assume that everything is fine if you disable the Hyper-V role.