If you have a legal copy, you ought to be able to call the Microsoft activation number (which can involve reading a lot of numbers over the phone), and they may be willing to fix the problem.
I suspect the problem stems from Windows trying to look at various attributes of the hardware and it's deduced, correctly or incorrectly, that it's not the same environment and therefore thinks you're trying to use two instances -or- that the installation changed enough that it simply wants you to revalidate.
That's gonna make it hard for you to resolve the problem yourself [legally].
In fairness, Microsoft's license may not want you to be able to do both with one copy of Windows.
This is the kind of licensing headache that makes OS X and Linux so attractive; you view yourself as one guy, the owner, who bought it, trying to use it on a single machine, and it's fighting you. Activations mean you're renting software, you just don't know for how long.