NQueue wrote: I have the Windows running in a separate compartment on the computer, rather than the mixed setup.
Really! What explicitly and specifically is that supposed to mean!? I guess you might mean a normal file based Virtual Machine vs. running a Boot Camp Windows install as a Virtual Machine?
I don't suppose that deleting the whole VM and reinstalling would deal with it?
If you delete an infected Virtual Machine then it gone, at least in that Virtual Machine, however if the Host became infected you'll need to deal with it as well.
Are you not running AntiVirus software in the Virtual Machine or Host?