I installed to a Boot Camp partition but had a similar issue. I had to contact Microsoft Technical Support and they had to give me the steps to make the key look valid to my system, then I could register it online. Not sure the reason but apparently there are a lot of issues registering Windows 7.
On the plus side I have it registered from the Boot Camp partition, and I was also able to register it in Parallels. It's seen as 2 installs to Windows, but the tech support people gave me the phone registration so I could also register it in Parallels.
I've heard horrible things about Microsoft in the past, but both my interactions with them were positive. I know technically Boot Camp and a virtual install could be considered 2 installs on the same computer, but they did not hassle me about using the same license for both.
