There was a bug in the Visual Studio template installer that shipped with the WPF/E December CTP SDK. The bug causes the uninstaller to check for the VS web application project (WAP) support. Since Visual Studio 2005 SP1 includes WAP support the WPF/E templates continued to work fine, right until you want to install them. The ultra painful workaround is to uninstall SP1, reinstall WAP support, uninstall the WPF/E tempaltes, uninstall WAP support and reinstall SP1. That really sucks.
Dave Wilson from our SDK team fully grasps the magnitude of badness and has written a blog post outlining a better workaround. Essentailly, you just need to add the one reg key the isntaller looks for. Dave even included a .reg file you can use to automate the process.