I had OroborOSX (XDarwin's nice window manager and launcher) constantly hanging at startup since installing Jaguar. I checked the various sources of help and finally found the solution in this thread on the SourceForge forums (go to the end of the thread...).
Basically, it comes from a conflict between Unsanity's APE (Application Enhancer, used for FruitMenu, WindowShade, etc.) and XDarwin. Excluding OroborOSX from the applications that are "enhanced" by FruitMenu, WindowShade or any of the Unsanity's PrefPanels restores OroborOSX functionality.
Hope they get this thing fixed soon!
Mac OS X Hints
http://hints.macworld.com/article.php?story=20020925060739148