Hello,
I've installed Windows 7 x64 in a VM and updated it until SP1 and tried to install Qubes Windows Tools 4.0.1-3. I get to the part where it says it will place some data on the E: drive and asks me to restart the VM, but when I do restart, Windows won't boot and keeps launching Startup Repair, though I do get entries for explorer.exe and others in the Qubes start menu.
A possible bug: when Qubes Tools give the notice about the E: drive I also get a Windows dialog box in the background asking me to format the E: drive (even though I can already access it from Windows Explorer). However, whether I do it or not, I still get stuck at Startup Repair on subsequent boots.
Zoid