Sometimes the registration process doesn't complete correctly unless you're running Sonar as Administrator. But this is only the case for plugins that you have to register by opening them in the host, e.g. Waves has its own License Center. I have my Waves license on a USB stick and it will check for it whenever I open a Waves plug, and otherwise just ignore it.
If you can't get your Waves license to stick I suggest taking it up with them, since it's a process completely separate from Sonar.