Just a thought
Consider using Parellels with the import option from the existing windows drive into your Mac OS. This way the Windows "partition" or VM if you will exists inside the Mac. Turn off sleep on the desktop - since the Windows will need to be a server (and maybe set the Parellels to boot up and logon the server admin when you restart the Mac). Then Time Machine on TC will do the full backup?
I have NO idea if this'll work but just a random thought.
I'm still new to Mac OS X - so take this with a jar of salt.