Arduino Due Windows 7 64bit drivers non working

OK so we have established it came from here so thats great news.

Running the IDE in a VM can present its own issues.

I gave up trying to use the XP mode VM bundled with windows 7 a long time ago for Arduinos and went to VMWARE which has better support for serial communications.

That may well be your issue.

Not sure why you would want to run it in a VM unless you are developing specifically for the XP platform and XP is known to have issues with some of the IDE's if you care to look that up in the forum.
There are some workarounds for XP but you may also be stuck with the serial issues in microsoft's own offering of a VM.

Any reason not to run it under windows 7 ?