Okay, I have done a little more testing scenarios. First on my Dell XPS Windows 7 SP1 64-bit, I found out the back USB ports are 3.0. Only the side port is USB 2.0. So previously I was only trying the back ports with my Due and Leonardo, both failed and got BSOD.
Now I tried multiple times the side USB 2.0 port and was able to get my Leonardo and Micro both to install the driver and work correctly with keyboard and mouse. Unfortunately my Due still died BSOD during the driver install. I think this could be because the HID emulation is not working correctly on the Due yet. So it may not be handshaking correctly with the driver install. (I say this because I have a couple of Windows XP SP3 32-bit systems that install the Due driver okay, and the SerialUSB works correctly, but the HID interface still never shows up.)
So for those of you with USB 3.0 ports, you may want to try it on USB 2.0 ports to see if it works any better, at least for the Leonardo and Micro. It would interesting if someone else can get the Due on a USB 2.0 port.