I had that very problem, as I had installed the original CTP and the April Refresh of the Windows Phone 7 Tools. Unfortunately, when I went to uninstall them (required to install the new stuff), the Microsoft Windows Phone 7 Tools ENU CTP just kept trying to reinstall everything.
Luckily, I found the XNA Game Studio Cleanup Tool at http://blogs.msdn.com/b/astebner/archive/2009/04/10/9544320.aspx and it nailed it. Just run the tool for Windows Phone and it will take care of the files and registry settings, and you’re good to go!