I have been researching on these forums and I have noticed a number of people having issues running 3.5/3.6 on Hyper-V. All the problems people document do exist but there is a very simple workaround.
Basically the solution is to first do a CD to HDD install of ZeroShell in a VMware environment. I then used a vmdk to vhd converter to convert the disk file and reload it in Hyper-V where it seems to work fine.
If anyone wants the detailed ‘howto’ then let me know and I will post further details.