I see that you narrowed this to the operating system, have you tried to contact Microsoft* about this?
I've tried Microsoft community forums with no success on my particular issue. All what they said to me so far is to use Windows 7/2008R2 instead of Windows 8, because these OSes don't have that problem on my machine.
But I'm developing software for Windows 8, which is much more comfortable from developer tools point of view to do from Windows 8 itself. I need Hyper-V to run software in emulator which comes with Windows 8 SDK.
I also develop some of system software, particularly virtual disk driver, which, unfortunately, can't be debugged in virtual machine. It currently relatively often makes host OS unresponsive, which forces me to reboot, which faces me the 5+ minutes boot time problem. (Just in case: the driver is not related to the boot time problem, as it repros on clean Windows 8 + Hyper-V installation).
Currently, I worked around this problem by creating a separate boot entry for my Windows 8 with disabled Hyper-V, so when I work on driver, I use that entry, and when I work on Windows 8 applications, I use boot entry with Hyper-V enabled.