The iPhone Dev Team has released PwnageTool 2.0.1 which addresses the following issues:
• It auto-finds the bl39 and bl46 files better, if they’re on your computer
• It creates the ~/Library/iTunes/Device Support/ folder if not present, which should help with some 1600 errors people have been having.
• Many people have reported the PwnageTool not starting up at all (the icon never stops bouncing). This issue should be resolved now.
• The Sparkle AppCast URL is fixed in this version, so automatic updates should work for future releases.
More info here.