First, I need to correct the apparent misconception that running Windows virtually from a partition is two installations. It's not. Your BootCamp install is one install. And Fusion can run that install virtually.
Nputer, your problem may be that you installed Windows with BootCamp, then installed it again using Fusion. You should instead install it with BootCamp, then set up Fusion to run Windows from the Windows partition.
Search the Fusion documentation for "create virtual machine from BootCamp partition."
EDIT: nope, I see you know about the BootCamp install. Read on then!
cleon, if the above applies, change your install...but it sounds like you did it correctly... The Fusion documentation talks about Windows wanting to reactivate every time you switch boot types (native or virtual). The important thing is to get VMWare Tools installed. Even if you did this already, there will be an "Update VMWare Tools" selection under the VMWare Fusion on the program menu. When you choose this option, you can Modify, Repair, or Uninstall. I recommend a Repair and that should take care of it.
It has happened to me that the VMWare installation did not complete or the registry got messed up somehow (it is Windows, after all).
Finally, to giulio: bootcamp still has it's place. I run Windows via Fusion for most little things, but it's nice to be able to reboot to native Windows in cases where a Windows app needs 3D graphics or other high RAM/CPU usage, and you can't/don't want to share the RAM with Mac for performance issues.